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sanger-pathogens / Roary

Rapid large-scale prokaryote pan genome analysis
http://sanger-pathogens.github.io/Roary
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Use of -e switch gives multifasta file with N's only #132

Closed dutchscientist closed 9 years ago

dutchscientist commented 9 years ago

I have Muscle and revtrans.py (v1.4) installed and in the PATH, but the .aln file produced contains only N's. The GFF's are from Prokka and work fine for creating the gene lists, but somewhere it goes wrong in the reverse translation.

Any thoughts?

The commandline is: roary -v -i 90 -e *.gff.

Edit: the temporary files are created fine, so the revtrans.py works fine, it is just in the conversion of all the temporary files to the final alignment which goes wrong

andrewjpage commented 9 years ago

One issue thats been reported a few days ago is that the gene names arent being extracted correctly from the gff files which I suspect would cause this bit to go haywire. I'll get a fix out for that in the next day or so, which will then hopefully solve things....

dutchscientist commented 9 years ago 
                                                                                  ‎Dear Andrew,Great. Do you want some of the files I am working with as example?Best wishesArnoud                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        From: andrewjpageSent: Monday, 1 June 2015 09:28To: sanger-pathogens/RoaryReply To: sanger-pathogens/RoaryCc: dutchscientistSubject: Re: [Roary] Use of -e switch gives multifasta file with N's only (#132)One issue thats been reported a few days ago is that the gene names arent being extracted correctly from the gff files which I suspect would cause this bit to go haywire. I'll get a fix out for that in the next day or so, which will then hopefully solve things....

—Reply to this email directly or view it on GitHub.

andrewjpage commented 9 years ago

Yea it would be great if you could send them to roary@sanger.ac.uk

Thanks a million.

dutchscientist commented 9 years ago

Have sent a small dataset (4 genomes) there, made using the don't delete switch.

On 1 June 2015 at 09:55, andrewjpage notifications@github.com wrote:

Yea it would be great if you could send them to roary@sanger.ac.uk

Thanks a million.

— Reply to this email directly or view it on GitHub https://github.com/sanger-pathogens/Roary/issues/132#issuecomment-107372236 .

andrewjpage commented 9 years ago

Hi, I've just updated Roary (version 3.0.0) which should hopefully resolve any issues you have. Instead of muscle and revtrans it uses PRANK which is properly packaged. You'll need to install prank first: apt-get install prank or brew install prank

then update Roary cpanm Bio::Roary

Regards, Andrew

On 1 June 2015 at 11:50, dutchscientist notifications@github.com wrote:

Have sent a small dataset (4 genomes) there, made using the don't delete switch.

On 1 June 2015 at 09:55, andrewjpage notifications@github.com wrote:

Yea it would be great if you could send them to roary@sanger.ac.uk

Thanks a million.

— Reply to this email directly or view it on GitHub < https://github.com/sanger-pathogens/Roary/issues/132#issuecomment-107372236

.

— Reply to this email directly or view it on GitHub https://github.com/sanger-pathogens/Roary/issues/132#issuecomment-107398104 .

dutchscientist commented 9 years ago

Great, will give that a go :-)

dutchscientist commented 9 years ago

Unfortunately I still get a file full of N's, despite installing prank.

I test with the set of Prokka 1.11-generated GFF files, which can be downloaded here: https://drive.google.com/file/d/0BzVZejrtim6RUnVBRUdrTWl2ZGs/view?usp=sharing (ZIP file with 4 GFF files included)

I do get the following text when installing via "sudo cpanm Bio::Roary" : --> Working on Bio::Roary Fetching http://www.cpan.org/authors/id/A/AJ/AJPAGE/Bio-Roary-3.0.2.tar.gz ... OK Configuring Bio-Roary-3.0.2 ... OK Building and testing Bio-Roary-3.0.2 ... FAIL ! Testing Bio-Roary-3.0.2 failed but installing it anyway. Successfully reinstalled Bio-Roary-3.0.2 1 distribution installed

Will try manual install as well.

dutchscientist commented 9 years ago

Everything else is working, despite the warning, including the addition of the annotation with the query_pan_genome

andrewjpage commented 9 years ago

Thanks for sending me the files. I'd be interested to know what tests are failing when Roary is installed,becuase that may well be the root cause (perhaps different versions of something). Would it be possible for you to reinstall it with the -v option (verbose) and send me the output? Thanks for helping me sort out the bugs.

On 13 June 2015 at 02:41, dutchscientist notifications@github.com wrote:

Unfortunately I still get a file full of N's, despite installing prank.

I test with the set of Prokka 1.11-generated GFF files, which can be downloaded here:

https://drive.google.com/file/d/0BzVZejrtim6RUnVBRUdrTWl2ZGs/view?usp=sharing (ZIP file with 4 GFF files included)

I do get the following text when installing via "sudo cpanm Bio::Roary" : --> Working on Bio::Roary Fetching http://www.cpan.org/authors/id/A/AJ/AJPAGE/Bio-Roary-3.0.2.tar.gz ... OK Configuring Bio-Roary-3.0.2 ... OK Building and testing Bio-Roary-3.0.2 ... FAIL ! Testing Bio-Roary-3.0.2 failed but installing it anyway. Successfully reinstalled Bio-Roary-3.0.2 1 distribution installed

Will try manual install as well.

— Reply to this email directly or view it on GitHub https://github.com/sanger-pathogens/Roary/issues/132#issuecomment-111651803 .

dutchscientist commented 9 years ago 
                                                                                  Hi Andrew,Yes, of course. Will do that tonight. Happy to help, I predict I will use it a lot!Arnoud                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        From: andrewjpageSent: Sunday, 14 June 2015 19:37To: sanger-pathogens/RoaryReply To: sanger-pathogens/RoaryCc: dutchscientistSubject: Re: [Roary] Use of -e switch gives multifasta file with N's only (#132)Thanks for sending me the files.

I'd be interested to know what tests are failing when Roary is installed,becuase that may well be the root cause (perhaps different versions of something). Would it be possible for you to reinstall it with the -v option (verbose) and send me the output? Thanks for helping me sort out the bugs.

On 13 June 2015 at 02:41, dutchscientist notifications@github.com wrote:

Unfortunately I still get a file full of N's, despite installing prank.

I test with the set of Prokka 1.11-generated GFF files, which can be downloaded here:

https://drive.google.com/file/d/0BzVZejrtim6RUnVBRUdrTWl2ZGs/view?usp=sharing (ZIP file with 4 GFF files included)

I do get the following text when installing via "sudo cpanm Bio::Roary" : --> Working on Bio::Roary Fetching http://www.cpan.org/authors/id/A/AJ/AJPAGE/Bio-Roary-3.0.2.tar.gz ... OK Configuring Bio-Roary-3.0.2 ... OK Building and testing Bio-Roary-3.0.2 ... FAIL ! Testing Bio-Roary-3.0.2 failed but installing it anyway. Successfully reinstalled Bio-Roary-3.0.2 1 distribution installed

Will try manual install as well.

— Reply to this email directly or view it on GitHub https://github.com/sanger-pathogens/Roary/issues/132#issuecomment-111651803 .

—Reply to this email directly or view it on GitHub.

dutchscientist commented 9 years ago

Hi Andrew,

this is the -v output.

--> Working on Bio::Roary

Fetching http://www.cpan.org/authors/id/A/AJ/AJPAGE/Bio-Roary-3.0.2.tar.gz ... OK

Bio-Roary-3.0.2/

Bio-Roary-3.0.2/AUTHORS

Bio-Roary-3.0.2/bin/

Bio-Roary-3.0.2/binaries/

Bio-Roary-3.0.2/contrib/

Bio-Roary-3.0.2/deployment_process

Bio-Roary-3.0.2/dist.ini

Bio-Roary-3.0.2/GPL-LICENSE

Bio-Roary-3.0.2/install_dependencies.sh

Bio-Roary-3.0.2/lib/

Bio-Roary-3.0.2/LICENSE

Bio-Roary-3.0.2/Makefile.PL

Bio-Roary-3.0.2/MANIFEST

Bio-Roary-3.0.2/META.yml

Bio-Roary-3.0.2/README

Bio-Roary-3.0.2/README.md

Bio-Roary-3.0.2/t/

Bio-Roary-3.0.2/t/bin/

Bio-Roary-3.0.2/t/Bio/

Bio-Roary-3.0.2/t/data/

Bio-Roary-3.0.2/t/dummy_blastp

Bio-Roary-3.0.2/t/dummy_cd-hit

Bio-Roary-3.0.2/t/dummy_makeblastdb

Bio-Roary-3.0.2/t/lib/

Bio-Roary-3.0.2/t/requires_external.t

Bio-Roary-3.0.2/t/lib/TestHelper.pm

Bio-Roary-3.0.2/t/data/accessory_graphs/

Bio-Roary-3.0.2/t/data/blast_results

Bio-Roary-3.0.2/t/data/clustered_proteins

Bio-Roary-3.0.2/t/data/clustered_proteins_pan_genome

Bio-Roary-3.0.2/t/data/clustered_proteins_post_analysis

Bio-Roary-3.0.2/t/data/clusters_input.fa

Bio-Roary-3.0.2/t/data/clusters_to_inflate

Bio-Roary-3.0.2/t/data/clusters_to_inflate.mcl

Bio-Roary-3.0.2/t/data/clusters_to_inflate_original_input.fa

Bio-Roary-3.0.2/t/data/clustersfile

Bio-Roary-3.0.2/t/data/core_alignment/

Bio-Roary-3.0.2/t/data/core_alignment.csv

Bio-Roary-3.0.2/t/data/core_alignment_core0.66.csv

Bio-Roary-3.0.2/t/data/core_group_statistics.csv

Bio-Roary-3.0.2/t/data/empty_file

Bio-Roary-3.0.2/t/data/example_1.faa

Bio-Roary-3.0.2/t/data/example_2.faa

Bio-Roary-3.0.2/t/data/example_3.faa

Bio-Roary-3.0.2/t/data/example_annotation.gff

Bio-Roary-3.0.2/t/data/example_annotation.gff.proteome.faa.expected

Bio-Roary-3.0.2/t/data/example_annotation_2.gff

Bio-Roary-3.0.2/t/data/example_groups

Bio-Roary-3.0.2/t/data/example_groups_without_labels

Bio-Roary-3.0.2/t/data/exp_qc_report.csv

Bio-Roary-3.0.2/t/data/exp_qc_report_real.csv

Bio-Roary-3.0.2/t/data/expected_0.seq

Bio-Roary-3.0.2/t/data/expected_5.seq

Bio-Roary-3.0.2/t/data/expected_clustered_proteins

Bio-Roary-3.0.2/t/data/expected_clusters_to_inflate

Bio-Roary-3.0.2/t/data/expected_combined_proteome.fa

Bio-Roary-3.0.2/t/data/expected_combined_proteome_with_filtering.fa

Bio-Roary-3.0.2/t/data/expected_complement_of_groups.gg

Bio-Roary-3.0.2/t/data/expected_complement_of_groups_core0.66.gg

Bio-Roary-3.0.2/t/data/expected_core_gene_alignment.aln

Bio-Roary-3.0.2/t/data/expected_core_gene_alignment_core0.66.aln

Bio-Roary-3.0.2/t/data/expected_create_pan_genome.fa

Bio-Roary-3.0.2/t/data/expected_example_annotation_1.faa

Bio-Roary-3.0.2/t/data/expected_filtered_original_input.fa

Bio-Roary-3.0.2/t/data/expected_gff_set_difference_common_set_statistics.csv

Bio-Roary-3.0.2/t/data/expected_group_labels

Bio-Roary-3.0.2/t/data/expected_group_statitics.csv

Bio-Roary-3.0.2/t/data/expected_group_statitics_missing_genes.csv

Bio-Roary-3.0.2/t/data/expected_group_statitics_verbose.csv

Bio-Roary-3.0.2/t/data/expected_inflated_results

Bio-Roary-3.0.2/t/data/expected_intersection_of_groups.gg

Bio-Roary-3.0.2/t/data/expected_intersection_of_groups_core0.66.gg

Bio-Roary-3.0.2/t/data/expected_nnn_at_end.fa

Bio-Roary-3.0.2/t/data/expected_nuc_multifasta.fa.aln

Bio-Roary-3.0.2/t/data/expected_nuc_multifasta.faa

Bio-Roary-3.0.2/t/data/expected_number_of_conserved_genes.tab

Bio-Roary-3.0.2/t/data/expected_number_of_conserved_genes_0.6.tab

Bio-Roary-3.0.2/t/data/expected_number_of_genes_in_pan_genome.tab

Bio-Roary-3.0.2/t/data/expected_number_of_new_genes.tab

Bio-Roary-3.0.2/t/data/expected_number_of_unique_genes.tab

Bio-Roary-3.0.2/t/data/expected_out_of_order_fasta.fa.sorted.fa

Bio-Roary-3.0.2/t/data/expected_output_core_missing_genes.aln

Bio-Roary-3.0.2/t/data/expected_output_filtered.fa

Bio-Roary-3.0.2/t/data/expected_output_groups

Bio-Roary-3.0.2/t/data/expected_output_groups_cdhit

Bio-Roary-3.0.2/t/data/expected_output_groups_group_2.fa

Bio-Roary-3.0.2/t/data/expected_output_groups_group_2_multi.fa

Bio-Roary-3.0.2/t/data/expected_output_groups_group_5.fa

Bio-Roary-3.0.2/t/data/expected_output_groups_group_5_multi.fa

Bio-Roary-3.0.2/t/data/expected_output_merged.aln

Bio-Roary-3.0.2/t/data/expected_output_merged_sparse.aln

Bio-Roary-3.0.2/t/data/expected_pan_genome.fa

Bio-Roary-3.0.2/t/data/expected_pan_genome_one_gene_per_fasta.fa

Bio-Roary-3.0.2/t/data/expected_pan_genome_reference.fa

Bio-Roary-3.0.2/t/data/expected_prank_input.fa.aln

Bio-Roary-3.0.2/t/data/expected_query_1.fna

Bio-Roary-3.0.2/t/data/expected_query_2.fna

Bio-Roary-3.0.2/t/data/expected_reannotated_groups_file

Bio-Roary-3.0.2/t/data/expected_set_difference_common_set

Bio-Roary-3.0.2/t/data/expected_set_difference_common_set_plot.png

Bio-Roary-3.0.2/t/data/expected_set_difference_common_set_statistics.csv

Bio-Roary-3.0.2/t/data/expected_set_difference_unique_set_one

Bio-Roary-3.0.2/t/data/expected_set_difference_unique_set_one_statistics.csv

Bio-Roary-3.0.2/t/data/expected_set_difference_unique_set_two

Bio-Roary-3.0.2/t/data/expected_set_difference_unique_set_two_plot.png

Bio-Roary-3.0.2/t/data/expected_set_difference_unique_set_two_statistics.csv

Bio-Roary-3.0.2/t/data/expected_uneven_sequences.fa

Bio-Roary-3.0.2/t/data/expected_union_of_groups.gg

Bio-Roary-3.0.2/t/data/genbank_gbff/

Bio-Roary-3.0.2/t/data/group_1.fa.aln

Bio-Roary-3.0.2/t/data/group_9.fa

Bio-Roary-3.0.2/t/data/kraken_report.txt

Bio-Roary-3.0.2/t/data/kraken_test/

Bio-Roary-3.0.2/t/data/locus_tag_gffs/

Bio-Roary-3.0.2/t/data/mcl_file

Bio-Roary-3.0.2/t/data/mdoH.fa.aln

Bio-Roary-3.0.2/t/data/multfasta1.aln

Bio-Roary-3.0.2/t/data/multfasta2.aln

Bio-Roary-3.0.2/t/data/multfasta3.aln

Bio-Roary-3.0.2/t/data/multfasta4.aln

Bio-Roary-3.0.2/t/data/multfasta5.aln

Bio-Roary-3.0.2/t/data/nnn_at_end.fa

Bio-Roary-3.0.2/t/data/nnn_at_end.fa.sorted.fa

Bio-Roary-3.0.2/t/data/nuc_multifasta.fa

Bio-Roary-3.0.2/t/data/nuc_to_be_aligned.fa

Bio-Roary-3.0.2/t/data/out_of_order_fasta.fa

Bio-Roary-3.0.2/t/data/out_of_order_fasta.fa.sorted.fa

Bio-Roary-3.0.2/t/data/overall_gene_presence_absence.csv

Bio-Roary-3.0.2/t/data/pan_genome_sequences/

Bio-Roary-3.0.2/t/data/post_analysis/

Bio-Roary-3.0.2/t/data/post_analysis_expected/

Bio-Roary-3.0.2/t/data/prank_input.fa

Bio-Roary-3.0.2/t/data/proteome_with_and_without_descriptions.faa

Bio-Roary-3.0.2/t/data/query_1.fa

Bio-Roary-3.0.2/t/data/query_1.gff

Bio-Roary-3.0.2/t/data/query_1_alternative_patterns.gff

Bio-Roary-3.0.2/t/data/query_2.fa

Bio-Roary-3.0.2/t/data/query_2.gff

Bio-Roary-3.0.2/t/data/query_3.fa

Bio-Roary-3.0.2/t/data/query_3.gff

Bio-Roary-3.0.2/t/data/query_4_missing_genes.fa

Bio-Roary-3.0.2/t/data/query_4_missing_genes.gff

Bio-Roary-3.0.2/t/data/query_5.gff

Bio-Roary-3.0.2/t/data/query_6.gff

Bio-Roary-3.0.2/t/data/query_groups

Bio-Roary-3.0.2/t/data/query_groups_all_merged

Bio-Roary-3.0.2/t/data/query_groups_missing_genes

Bio-Roary-3.0.2/t/data/raxml.tre

Bio-Roary-3.0.2/t/data/real_data_1.gff

Bio-Roary-3.0.2/t/data/real_data_2.gff

Bio-Roary-3.0.2/t/data/real_data_core_gene_alignment.aln

Bio-Roary-3.0.2/t/data/reformat_input_gffs/

Bio-Roary-3.0.2/t/data/reorder_isolates.tre

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_breadth_alpha.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_breadth_creation.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_breadth_height.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_breadth_revalpha.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_depth_alpha.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_depth_creation.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_depth_height.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_depth_revalpha.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_input.csv

Bio-Roary-3.0.2/t/data/sequences_with_unknowns.faa

Bio-Roary-3.0.2/t/data/shred1.gff

Bio-Roary-3.0.2/t/data/shred1.shred.fa

Bio-Roary-3.0.2/t/data/shred2.gff

Bio-Roary-3.0.2/t/data/shred2.shred.fa

Bio-Roary-3.0.2/t/data/sopB.fa.aln

Bio-Roary-3.0.2/t/data/speH.fa.aln

Bio-Roary-3.0.2/t/data/split_groups/

Bio-Roary-3.0.2/t/data/split_pan_genome_sequences/

Bio-Roary-3.0.2/t/data/uneven_sequences.fa

Bio-Roary-3.0.2/t/data/uneven_sequences.fa.sorted.fa

Bio-Roary-3.0.2/t/data/variable_core/

Bio-Roary-3.0.2/t/data/variable_core/gene_1.fa.aln

Bio-Roary-3.0.2/t/data/variable_core/gene_2.fa.aln

Bio-Roary-3.0.2/t/data/variable_core/gene_3.fa.aln

Bio-Roary-3.0.2/t/data/variable_core/gene_4.fa.aln

Bio-Roary-3.0.2/t/data/variable_core/gene_5.fa.aln

Bio-Roary-3.0.2/t/data/split_pan_genome_sequences/argF.fa

Bio-Roary-3.0.2/t/data/split_pan_genome_sequences/different.fa

Bio-Roary-3.0.2/t/data/split_pan_genome_sequences/hly.fa

Bio-Roary-3.0.2/t/data/split_pan_genome_sequences/reannotated_groups_file

Bio-Roary-3.0.2/t/data/split_pan_genome_sequences/speH.fa

Bio-Roary-3.0.2/t/data/split_groups/paralog_clusters1

Bio-Roary-3.0.2/t/data/split_groups/paralog_clusters2

Bio-Roary-3.0.2/t/data/split_groups/paralog_clusters3

Bio-Roary-3.0.2/t/data/split_groups/paralog_clusters4

Bio-Roary-3.0.2/t/data/split_groups/paralog_exp_clusters1

Bio-Roary-3.0.2/t/data/split_groups/paralog_exp_clusters2

Bio-Roary-3.0.2/t/data/split_groups/paralog_exp_clusters3

Bio-Roary-3.0.2/t/data/split_groups/paralog_exp_clusters4

Bio-Roary-3.0.2/t/data/split_groups/paralogs1.fa

Bio-Roary-3.0.2/t/data/split_groups/paralogs2.fa

Bio-Roary-3.0.2/t/data/split_groups/paralogs3.fa

Bio-Roary-3.0.2/t/data/reformat_input_gffs/expected_fixed_query_2.gff

Bio-Roary-3.0.2/t/data/reformat_input_gffs/expected_fixed_query_3.gff

Bio-Roary-3.0.2/t/data/reformat_input_gffs/expected_real_1.gff

Bio-Roary-3.0.2/t/data/reformat_input_gffs/query_1.gff

Bio-Roary-3.0.2/t/data/reformat_input_gffs/query_2.gff

Bio-Roary-3.0.2/t/data/reformat_input_gffs/query_3.gff

Bio-Roary-3.0.2/t/data/reformat_input_gffs/real_1.gff

Bio-Roary-3.0.2/t/data/post_analysis_expected/accessory.header.embl

Bio-Roary-3.0.2/t/data/post_analysis_expected/accessory.tab

Bio-Roary-3.0.2/t/data/post_analysis_expected/core_accessory.header.embl

Bio-Roary-3.0.2/t/data/post_analysis_expected/core_accessory.tab

Bio-Roary-3.0.2/t/data/post_analysis_expected/gene_presence_absence.csv

Bio-Roary-3.0.2/t/data/post_analysis/_clustered

Bio-Roary-3.0.2/t/data/post_analysis/_clustered.bak.clstr

Bio-Roary-3.0.2/t/data/post_analysis/_clustered.clstr

Bio-Roary-3.0.2/t/data/post_analysis/_combined_files

Bio-Roary-3.0.2/t/data/post_analysis/_combined_files.groups

Bio-Roary-3.0.2/t/data/post_analysis/_fasta_files

Bio-Roary-3.0.2/t/data/post_analysis/_gff_files

Bio-Roary-3.0.2/t/data/post_analysis/_uninflated_mcl_groups

Bio-Roary-3.0.2/t/data/post_analysis/query_1.gff.proteome.faa

Bio-Roary-3.0.2/t/data/post_analysis/query_2.gff.proteome.faa

Bio-Roary-3.0.2/t/data/post_analysis/query_6.gff.proteome.faa

Bio-Roary-3.0.2/t/data/pan_genome_sequences/argF.fa

Bio-Roary-3.0.2/t/data/pan_genome_sequences/hly.fa

Bio-Roary-3.0.2/t/data/pan_genome_sequences/speH.fa

Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_1.gff

Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_1.gff.proteome.faa.expected

Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_2.gff

Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_2.gff.proteome.faa.expected

Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_3.gff

Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_3.gff.proteome.faa.expected

Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_5.gff

Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_5.gff.proteome.faa.expected

Bio-Roary-3.0.2/t/data/kraken_test/database.idx

Bio-Roary-3.0.2/t/data/kraken_test/database.jdb

Bio-Roary-3.0.2/t/data/kraken_test/database.kdb

Bio-Roary-3.0.2/t/data/kraken_test/taxonomy/

Bio-Roary-3.0.2/t/data/kraken_test/taxonomy/names.dmp

Bio-Roary-3.0.2/t/data/kraken_test/taxonomy/nodes.dmp

Bio-Roary-3.0.2/t/data/genbank_gbff/genbank1.gff

Bio-Roary-3.0.2/t/data/genbank_gbff/genbank1.gff.proteome.faa.expected

Bio-Roary-3.0.2/t/data/genbank_gbff/genbank2.gff

Bio-Roary-3.0.2/t/data/genbank_gbff/genbank2.gff.proteome.faa.expected

Bio-Roary-3.0.2/t/data/genbank_gbff/genbank3.gff

Bio-Roary-3.0.2/t/data/genbank_gbff/genbank3.gff.proteome.faa.expected

Bio-Roary-3.0.2/t/data/genbank_gbff/genbank_gene_presence_absence.csv

Bio-Roary-3.0.2/t/data/core_alignment/argF.fa.aln

Bio-Roary-3.0.2/t/data/core_alignment/hly.fa.aln

Bio-Roary-3.0.2/t/data/core_alignment/speH.fa.aln

Bio-Roary-3.0.2/t/data/accessory_graphs/core_deletion

Bio-Roary-3.0.2/t/data/accessory_graphs/core_island

Bio-Roary-3.0.2/t/data/accessory_graphs/file_1.fa

Bio-Roary-3.0.2/t/data/accessory_graphs/file_1.gff

Bio-Roary-3.0.2/t/data/accessory_graphs/file_2.fa

Bio-Roary-3.0.2/t/data/accessory_graphs/file_2.gff

Bio-Roary-3.0.2/t/data/accessory_graphs/file_3.fa

Bio-Roary-3.0.2/t/data/accessory_graphs/file_3.gff

Bio-Roary-3.0.2/t/data/accessory_graphs/no_accessory

Bio-Roary-3.0.2/t/data/accessory_graphs/one_branch

Bio-Roary-3.0.2/t/data/accessory_graphs/one_bubble

Bio-Roary-3.0.2/t/data/accessory_graphs/single_gene_contig

Bio-Roary-3.0.2/t/data/accessory_graphs/two_graphs

Bio-Roary-3.0.2/t/Bio/Roary/

Bio-Roary-3.0.2/t/Bio/Roary/AnalyseGroups.t

Bio-Roary-3.0.2/t/Bio/Roary/AnnotateGroups.t

Bio-Roary-3.0.2/t/Bio/Roary/ChunkFastaFile.t

Bio-Roary-3.0.2/t/Bio/Roary/CombinedProteome.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/

Bio-Roary-3.0.2/t/Bio/Roary/ContigsToGeneIDsFromGFF.t

Bio-Roary-3.0.2/t/Bio/Roary/External/

Bio-Roary-3.0.2/t/Bio/Roary/ExtractCoreGenesFromSpreadsheet.t

Bio-Roary-3.0.2/t/Bio/Roary/ExtractProteomeFromGFFs.t

Bio-Roary-3.0.2/t/Bio/Roary/FilterFullClusters.t

Bio-Roary-3.0.2/t/Bio/Roary/GeneNamesFromGFF.t

Bio-Roary-3.0.2/t/Bio/Roary/GroupLabels.t

Bio-Roary-3.0.2/t/Bio/Roary/GroupStatistics.t

Bio-Roary-3.0.2/t/Bio/Roary/InflateClusters.t

Bio-Roary-3.0.2/t/Bio/Roary/OrderGenes.t

Bio-Roary-3.0.2/t/Bio/Roary/Output/

Bio-Roary-3.0.2/t/Bio/Roary/ParallelAllAgainstAllBlast.t

Bio-Roary-3.0.2/t/Bio/Roary/PrepareInputFiles.t

Bio-Roary-3.0.2/t/Bio/Roary/QC/

Bio-Roary-3.0.2/t/Bio/Roary/ReformatInputGFFs.t

Bio-Roary-3.0.2/t/Bio/Roary/ReorderSpreadsheet.t

Bio-Roary-3.0.2/t/Bio/Roary/SampleOrder.t

Bio-Roary-3.0.2/t/Bio/Roary/SequenceLengths.t

Bio-Roary-3.0.2/t/Bio/Roary/SortFasta.t

Bio-Roary-3.0.2/t/Bio/Roary/SplitGroups.t

Bio-Roary-3.0.2/t/Bio/Roary/QC/Report.t

Bio-Roary-3.0.2/t/Bio/Roary/Output/DifferenceBetweenSets.t

Bio-Roary-3.0.2/t/Bio/Roary/Output/GroupsMultifastaProtein.t

Bio-Roary-3.0.2/t/Bio/Roary/Output/GroupsMultifastas.t

Bio-Roary-3.0.2/t/Bio/Roary/Output/GroupsMultifastasNucleotide.t

Bio-Roary-3.0.2/t/Bio/Roary/Output/NumberOfGroups.t

Bio-Roary-3.0.2/t/Bio/Roary/Output/QueryGroups.t

Bio-Roary-3.0.2/t/Bio/Roary/External/Blastp.t

Bio-Roary-3.0.2/t/Bio/Roary/External/Cdhit.t

Bio-Roary-3.0.2/t/Bio/Roary/External/Makeblastdb.t

Bio-Roary-3.0.2/t/Bio/Roary/External/Mcl.t

Bio-Roary-3.0.2/t/Bio/Roary/External/Prank.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/ExtractProteomeFromGff.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/QueryRoary.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/Roary.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/RoaryCoreAlignment.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/RoaryPostAnalysis.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/TransferAnnotationToGroups.t

Bio-Roary-3.0.2/t/bin/dummy_blastp

Bio-Roary-3.0.2/t/bin/dummy_cd-hit

Bio-Roary-3.0.2/t/bin/dummy_makeblastdb

Bio-Roary-3.0.2/t/bin/dummy_mcl

Bio-Roary-3.0.2/t/bin/dummy_mcxdeblast

Bio-Roary-3.0.2/t/bin/dummy_segmasker

Bio-Roary-3.0.2/lib/Bio/

Bio-Roary-3.0.2/lib/Bio/Roary/

Bio-Roary-3.0.2/lib/Bio/Roary.pm

Bio-Roary-3.0.2/lib/Bio/Roary/AnalyseGroups.pm

Bio-Roary-3.0.2/lib/Bio/Roary/AnnotateGroups.pm

Bio-Roary-3.0.2/lib/Bio/Roary/BedFromGFFRole.pm

Bio-Roary-3.0.2/lib/Bio/Roary/ChunkFastaFile.pm

Bio-Roary-3.0.2/lib/Bio/Roary/ClustersRole.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CombinedProteome.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/

Bio-Roary-3.0.2/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Exceptions.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/

Bio-Roary-3.0.2/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm

Bio-Roary-3.0.2/lib/Bio/Roary/ExtractProteomeFromGFF.pm

Bio-Roary-3.0.2/lib/Bio/Roary/ExtractProteomeFromGFFs.pm

Bio-Roary-3.0.2/lib/Bio/Roary/FilterFullClusters.pm

Bio-Roary-3.0.2/lib/Bio/Roary/FilterUnknownsFromFasta.pm

Bio-Roary-3.0.2/lib/Bio/Roary/GeneNamesFromGFF.pm

Bio-Roary-3.0.2/lib/Bio/Roary/GroupLabels.pm

Bio-Roary-3.0.2/lib/Bio/Roary/GroupStatistics.pm

Bio-Roary-3.0.2/lib/Bio/Roary/InflateClusters.pm

Bio-Roary-3.0.2/lib/Bio/Roary/IterativeCdhit.pm

Bio-Roary-3.0.2/lib/Bio/Roary/JobRunner/

Bio-Roary-3.0.2/lib/Bio/Roary/LookupGeneFiles.pm

Bio-Roary-3.0.2/lib/Bio/Roary/MergeMultifastaAlignments.pm

Bio-Roary-3.0.2/lib/Bio/Roary/OrderGenes.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/

Bio-Roary-3.0.2/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm

Bio-Roary-3.0.2/lib/Bio/Roary/ParseGFFAnnotationRole.pm

Bio-Roary-3.0.2/lib/Bio/Roary/PostAnalysis.pm

Bio-Roary-3.0.2/lib/Bio/Roary/PrepareInputFiles.pm

Bio-Roary-3.0.2/lib/Bio/Roary/QC/

Bio-Roary-3.0.2/lib/Bio/Roary/ReformatInputGFFs.pm

Bio-Roary-3.0.2/lib/Bio/Roary/ReorderSpreadsheet.pm

Bio-Roary-3.0.2/lib/Bio/Roary/SampleOrder.pm

Bio-Roary-3.0.2/lib/Bio/Roary/SequenceLengths.pm

Bio-Roary-3.0.2/lib/Bio/Roary/SortFasta.pm

Bio-Roary-3.0.2/lib/Bio/Roary/SplitGroups.pm

Bio-Roary-3.0.2/lib/Bio/Roary/QC/Report.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/BlastIdentityFrequency.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/DifferenceBetweenSets.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/EmblGroups.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/GroupMultifasta.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/GroupsMultifastas.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/NumberOfGroups.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/QueryGroups.pm

Bio-Roary-3.0.2/lib/Bio/Roary/JobRunner/Local.pm

Bio-Roary-3.0.2/lib/Bio/Roary/JobRunner/Parallel.pm

Bio-Roary-3.0.2/lib/Bio/Roary/JobRunner/Role.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/Blastp.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/Cdhit.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/IterativeCdhit.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/Makeblastdb.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/Mcl.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/PostAnalysis.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/Prank.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/ProteinMuscleAlignmentFromNucleotides.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/Common.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/CreatePanGenome.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/IterativeCdhit.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/QueryRoary.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/Roary.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm

Bio-Roary-3.0.2/contrib/roary_plots/

Bio-Roary-3.0.2/contrib/roary_plots/README.md

Bio-Roary-3.0.2/contrib/roary_plots/roary.html

Bio-Roary-3.0.2/contrib/roary_plots/roary_files/

Bio-Roary-3.0.2/contrib/roary_plots/roary_plots.ipynb

Bio-Roary-3.0.2/contrib/roary_plots/roary_plots.py

Bio-Roary-3.0.2/contrib/roary_plots/roary_files/jquery.min.js

Bio-Roary-3.0.2/contrib/roary_plots/roary_files/MathJax.js

Bio-Roary-3.0.2/contrib/roary_plots/roary_files/require.min.js

Bio-Roary-3.0.2/binaries/darwin/

Bio-Roary-3.0.2/binaries/linux/

Bio-Roary-3.0.2/binaries/linux/bedtools

Bio-Roary-3.0.2/binaries/linux/blastp

Bio-Roary-3.0.2/binaries/linux/cd-hit

Bio-Roary-3.0.2/binaries/linux/makeblastdb

Bio-Roary-3.0.2/binaries/linux/mcl

Bio-Roary-3.0.2/binaries/linux/mcxdeblast

Bio-Roary-3.0.2/binaries/linux/parallel

Bio-Roary-3.0.2/binaries/linux/prank

Bio-Roary-3.0.2/binaries/darwin/bedtools

Bio-Roary-3.0.2/binaries/darwin/blastp

Bio-Roary-3.0.2/binaries/darwin/cd-hit

Bio-Roary-3.0.2/binaries/darwin/makeblastdb

Bio-Roary-3.0.2/binaries/darwin/mcl

Bio-Roary-3.0.2/binaries/darwin/mcxdeblast

Bio-Roary-3.0.2/binaries/darwin/parallel

Bio-Roary-3.0.2/binaries/darwin/prank

Bio-Roary-3.0.2/bin/create_pan_genome

Bio-Roary-3.0.2/bin/create_pan_genome_plots.R

Bio-Roary-3.0.2/bin/extract_proteome_from_gff

Bio-Roary-3.0.2/bin/iterative_cdhit

Bio-Roary-3.0.2/bin/pan_genome_core_alignment

Bio-Roary-3.0.2/bin/pan_genome_post_analysis

Bio-Roary-3.0.2/bin/pan_genome_reorder_spreadsheet

Bio-Roary-3.0.2/bin/parallel_all_against_all_blastp

Bio-Roary-3.0.2/bin/protein_muscle_alignment_from_nucleotides

Bio-Roary-3.0.2/bin/query_pan_genome

Bio-Roary-3.0.2/bin/roary

Bio-Roary-3.0.2/bin/transfer_annotation_to_groups

Configuring Bio-Roary-3.0.2 ... Checking if your kit is complete...

Looks good

Generating a Unix-style Makefile

Writing Makefile for Bio::Roary

Writing MYMETA.yml and MYMETA.json

OK

Building and testing Bio-Roary-3.0.2 ... cp lib/Bio/Roary/External/IterativeCdhit.pm blib/lib/Bio/Roary/External/IterativeCdhit.pm

cp lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm blib/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm

cp lib/Bio/Roary/CommandLine/IterativeCdhit.pm blib/lib/Bio/Roary/CommandLine/IterativeCdhit.pm

cp lib/Bio/Roary.pm blib/lib/Bio/Roary.pm

cp lib/Bio/Roary/CommandLine/QueryRoary.pm blib/lib/Bio/Roary/CommandLine/QueryRoary.pm

cp lib/Bio/Roary/CombinedProteome.pm blib/lib/Bio/Roary/CombinedProteome.pm

cp lib/Bio/Roary/ChunkFastaFile.pm blib/lib/Bio/Roary/ChunkFastaFile.pm

cp lib/Bio/Roary/CommandLine/Roary.pm blib/lib/Bio/Roary/CommandLine/Roary.pm

cp lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm blib/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm

cp lib/Bio/Roary/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm

cp lib/Bio/Roary/Exceptions.pm blib/lib/Bio/Roary/Exceptions.pm

cp lib/Bio/Roary/External/Cdhit.pm blib/lib/Bio/Roary/External/Cdhit.pm

cp lib/Bio/Roary/CommandLine/Common.pm blib/lib/Bio/Roary/CommandLine/Common.pm

cp lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm blib/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm

cp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.pm

cp lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm

cp lib/Bio/Roary/External/Blastp.pm blib/lib/Bio/Roary/External/Blastp.pm

cp lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm

cp lib/Bio/Roary/External/Prank.pm blib/lib/Bio/Roary/External/Prank.pm

cp lib/Bio/Roary/CommandLine/CreatePanGenome.pm blib/lib/Bio/Roary/CommandLine/CreatePanGenome.pm

cp lib/Bio/Roary/ClustersRole.pm blib/lib/Bio/Roary/ClustersRole.pm

cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm

cp lib/Bio/Roary/AnnotateGroups.pm blib/lib/Bio/Roary/AnnotateGroups.pm

cp lib/Bio/Roary/External/Mcl.pm blib/lib/Bio/Roary/External/Mcl.pm

cp lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm blib/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm

cp lib/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.pm blib/lib/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.pm

cp lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm blib/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm

cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.pm

cp lib/Bio/Roary/External/ProteinMuscleAlignmentFromNucleotides.pm blib/lib/Bio/Roary/External/ProteinMuscleAlignmentFromNucleotides.pm

cp lib/Bio/Roary/External/Makeblastdb.pm blib/lib/Bio/Roary/External/Makeblastdb.pm

cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.pm

cp lib/Bio/Roary/GeneNamesFromGFF.pm blib/lib/Bio/Roary/GeneNamesFromGFF.pm

cp lib/Bio/Roary/ExtractProteomeFromGFF.pm blib/lib/Bio/Roary/ExtractProteomeFromGFF.pm

cp lib/Bio/Roary/JobRunner/Local.pm blib/lib/Bio/Roary/JobRunner/Local.pm

cp lib/Bio/Roary/Output/GroupsMultifastaProtein.pm blib/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm

cp lib/Bio/Roary/ExtractProteomeFromGFFs.pm blib/lib/Bio/Roary/ExtractProteomeFromGFFs.pm

cp lib/Bio/Roary/ReorderSpreadsheet.pm blib/lib/Bio/Roary/ReorderSpreadsheet.pm

cp lib/Bio/Roary/QC/Report.pm blib/lib/Bio/Roary/QC/Report.pm

cp lib/Bio/Roary/Output/EmblGroups.pm blib/lib/Bio/Roary/Output/EmblGroups.pm

cp lib/Bio/Roary/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm

cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm blib/lib/Bio/Roary/Output/DifferenceBetweenSets.pm

cp lib/Bio/Roary/Output/GroupsMultifastas.pm blib/lib/Bio/Roary/Output/GroupsMultifastas.pm

cp lib/Bio/Roary/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm

cp lib/Bio/Roary/Output/GroupMultifasta.pm blib/lib/Bio/Roary/Output/GroupMultifasta.pm

cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm

cp lib/Bio/Roary/Output/QueryGroups.pm blib/lib/Bio/Roary/Output/QueryGroups.pm

cp lib/Bio/Roary/Output/NumberOfGroups.pm blib/lib/Bio/Roary/Output/NumberOfGroups.pm

cp lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm

cp lib/Bio/Roary/GroupLabels.pm blib/lib/Bio/Roary/GroupLabels.pm

cp lib/Bio/Roary/JobRunner/Parallel.pm blib/lib/Bio/Roary/JobRunner/Parallel.pm

cp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm

cp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm

cp lib/Bio/Roary/FilterFullClusters.pm blib/lib/Bio/Roary/FilterFullClusters.pm

cp lib/Bio/Roary/MergeMultifastaAlignments.pm blib/lib/Bio/Roary/MergeMultifastaAlignments.pm

cp lib/Bio/Roary/PostAnalysis.pm blib/lib/Bio/Roary/PostAnalysis.pm

cp lib/Bio/Roary/PrepareInputFiles.pm blib/lib/Bio/Roary/PrepareInputFiles.pm

cp lib/Bio/Roary/Output/BlastIdentityFrequency.pm blib/lib/Bio/Roary/Output/BlastIdentityFrequency.pm

cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm

cp lib/Bio/Roary/JobRunner/Role.pm blib/lib/Bio/Roary/JobRunner/Role.pm

cp lib/Bio/Roary/InflateClusters.pm blib/lib/Bio/Roary/InflateClusters.pm

cp lib/Bio/Roary/OrderGenes.pm blib/lib/Bio/Roary/OrderGenes.pm

cp lib/Bio/Roary/FilterUnknownsFromFasta.pm blib/lib/Bio/Roary/FilterUnknownsFromFasta.pm

cp lib/Bio/Roary/SplitGroups.pm blib/lib/Bio/Roary/SplitGroups.pm

cp lib/Bio/Roary/SortFasta.pm blib/lib/Bio/Roary/SortFasta.pm

cp lib/Bio/Roary/SampleOrder.pm blib/lib/Bio/Roary/SampleOrder.pm

cp lib/Bio/Roary/SequenceLengths.pm blib/lib/Bio/Roary/SequenceLengths.pm

cp bin/pan_genome_reorder_spreadsheet blib/script/pan_genome_reorder_spreadsheet

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_reorder_spreadsheet

cp bin/iterative_cdhit blib/script/iterative_cdhit

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/iterative_cdhit

cp bin/create_pan_genome blib/script/create_pan_genome

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome

cp bin/query_pan_genome blib/script/query_pan_genome

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/query_pan_genome

cp bin/roary blib/script/roary

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary

cp bin/transfer_annotation_to_groups blib/script/transfer_annotation_to_groups

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/transfer_annotation_to_groups

cp bin/create_pan_genome_plots.R blib/script/create_pan_genome_plots.R

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome_plots.R

cp bin/pan_genome_post_analysis blib/script/pan_genome_post_analysis

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_post_analysis

cp bin/pan_genome_core_alignment blib/script/pan_genome_core_alignment

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_core_alignment

cp bin/parallel_all_against_all_blastp blib/script/parallel_all_against_all_blastp

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/parallel_all_against_all_blastp

cp bin/protein_muscle_alignment_from_nucleotides blib/script/protein_muscle_alignment_from_nucleotides

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/protein_muscle_alignment_from_nucleotides

cp bin/extract_proteome_from_gff blib/script/extract_proteome_from_gff

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/extract_proteome_from_gff

Manifying 12 pod documents

Manifying 26 pod documents

Manifying 26 pod documents

Manifying 14 pod documents

PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef _Test::Harness::Switches; testharness(0, 'blib/lib', 'blib/arch')" t/.t t/Bio/Roary/.t t/Bio/Roary/CommandLine/.t t/Bio/Roary/External/.t t/Bio/Roary/Output/.t t/Bio/Roary/QC/*.t

t/Bio/Roary/AnalyseGroups.t ...................................... ok

t/Bio/Roary/AnnotateGroups.t ..................................... ok

t/Bio/Roary/ChunkFastaFile.t ..................................... ok

t/Bio/Roary/CombinedProteome.t ................................... ok

t/Bio/Roary/CommandLine/ExtractProteomeFromGff.t ................. ok

t/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.t ............ ok

t/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.t .. ok

t/Bio/Roary/CommandLine/QueryRoary.t ............................. ok

t/Bio/Roary/CommandLine/Roary.t ..................................

Dubious, test returned 2 (wstat 512, 0x200)

Failed 1/9 subtests

t/Bio/Roary/CommandLine/RoaryCoreAlignment.t ..................... ok

t/Bio/Roary/CommandLine/RoaryPostAnalysis.t ...................... ok

t/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.t ................ ok

t/Bio/Roary/CommandLine/TransferAnnotationToGroups.t ............. ok

t/Bio/Roary/ContigsToGeneIDsFromGFF.t ............................ ok

t/Bio/Roary/External/Blastp.t .................................... ok

t/Bio/Roary/External/Cdhit.t ..................................... ok

t/Bio/Roary/External/Makeblastdb.t ............................... ok

t/Bio/Roary/External/Mcl.t ....................................... ok

t/Bio/Roary/External/Prank.t ..................................... ok

t/Bio/Roary/ExtractCoreGenesFromSpreadsheet.t .................... ok

t/Bio/Roary/ExtractProteomeFromGFFs.t ............................ ok

t/Bio/Roary/FilterFullClusters.t ................................. ok

t/Bio/Roary/GeneNamesFromGFF.t ................................... ok

t/Bio/Roary/GroupLabels.t ........................................ ok

t/Bio/Roary/GroupStatistics.t .................................... ok

t/Bio/Roary/InflateClusters.t .................................... ok

t/Bio/Roary/OrderGenes.t ......................................... ok

t/Bio/Roary/Output/DifferenceBetweenSets.t ....................... ok

t/Bio/Roary/Output/GroupsMultifastaProtein.t ..................... ok

t/Bio/Roary/Output/GroupsMultifastas.t ........................... ok

t/Bio/Roary/Output/GroupsMultifastasNucleotide.t ................. ok

t/Bio/Roary/Output/NumberOfGroups.t .............................. ok

t/Bio/Roary/Output/QueryGroups.t ................................. ok

t/Bio/Roary/ParallelAllAgainstAllBlast.t ......................... ok

t/Bio/Roary/PrepareInputFiles.t .................................. ok

t/Bio/Roary/QC/Report.t .......................................... ok

t/Bio/Roary/ReformatInputGFFs.t .................................. ok

t/Bio/Roary/ReorderSpreadsheet.t ................................. ok

t/Bio/Roary/SampleOrder.t ........................................ ok

t/Bio/Roary/SequenceLengths.t .................................... ok

t/Bio/Roary/SortFasta.t .......................................... ok

t/Bio/Roary/SplitGroups.t ........................................ ok

t/requires_external.t ............................................ ok

Test Summary Report

t/Bio/Roary/CommandLine/Roary.t (Wstat: 512 Tests: 9 Failed: 1)

Failed test: 9

Non-zero exit status: 2

Parse errors: No plan found in TAP output

Files=43, Tests=572, 70 wallclock secs ( 0.30 usr 0.08 sys + 62.44 cusr 7.66 csys = 70.48 CPU)

Result: FAIL

FAIL

Manifying 12 pod documents

Manifying 26 pod documents

Manifying 26 pod documents

Manifying 14 pod documents

Appending installation info to /usr/lib/perl/5.18/perllocal.pod

Successfully reinstalled Bio-Roary-3.0.2

Installing /usr/local/share/perl/5.18.2/x86_64-linux-gnu-thread-multi/.meta/Bio-Roary-3.0.2/install.json

1 distribution installed

andrewjpage commented 9 years ago

Thanks Arnoud for the output. I 'think' I know which tests is failing, but I was wondering if you could download the code and run the individual test which would give specific output? The commands are:

git clone https://github.com/sanger-pathogens/Roary.git cd Roary perl t/Bio/Roary/CommandLine/Roary.t

Thanks again for your time, your building up a lot of beer miles here!

On 14 June 2015 at 19:48, dutchscientist notifications@github.com wrote:

Hi Andrew,

this is the -v output.

--> Working on Bio::Roary

Fetching http://www.cpan.org/authors/id/A/AJ/AJPAGE/Bio-Roary-3.0.2.tar.gz ... OK

Bio-Roary-3.0.2/

Bio-Roary-3.0.2/AUTHORS

Bio-Roary-3.0.2/bin/

Bio-Roary-3.0.2/binaries/

Bio-Roary-3.0.2/contrib/

Bio-Roary-3.0.2/deployment_process

Bio-Roary-3.0.2/dist.ini

Bio-Roary-3.0.2/GPL-LICENSE

Bio-Roary-3.0.2/install_dependencies.sh

Bio-Roary-3.0.2/lib/

Bio-Roary-3.0.2/LICENSE

Bio-Roary-3.0.2/Makefile.PL

Bio-Roary-3.0.2/MANIFEST

Bio-Roary-3.0.2/META.yml

Bio-Roary-3.0.2/README

Bio-Roary-3.0.2/README.md

Bio-Roary-3.0.2/t/

Bio-Roary-3.0.2/t/bin/

Bio-Roary-3.0.2/t/Bio/

Bio-Roary-3.0.2/t/data/

Bio-Roary-3.0.2/t/dummy_blastp

Bio-Roary-3.0.2/t/dummy_cd-hit

Bio-Roary-3.0.2/t/dummy_makeblastdb

Bio-Roary-3.0.2/t/lib/

Bio-Roary-3.0.2/t/requires_external.t

Bio-Roary-3.0.2/t/lib/TestHelper.pm

Bio-Roary-3.0.2/t/data/accessory_graphs/

Bio-Roary-3.0.2/t/data/blast_results

Bio-Roary-3.0.2/t/data/clustered_proteins

Bio-Roary-3.0.2/t/data/clustered_proteins_pan_genome

Bio-Roary-3.0.2/t/data/clustered_proteins_post_analysis

Bio-Roary-3.0.2/t/data/clusters_input.fa

Bio-Roary-3.0.2/t/data/clusters_to_inflate

Bio-Roary-3.0.2/t/data/clusters_to_inflate.mcl

Bio-Roary-3.0.2/t/data/clusters_to_inflate_original_input.fa

Bio-Roary-3.0.2/t/data/clustersfile

Bio-Roary-3.0.2/t/data/core_alignment/

Bio-Roary-3.0.2/t/data/core_alignment.csv

Bio-Roary-3.0.2/t/data/core_alignment_core0.66.csv

Bio-Roary-3.0.2/t/data/core_group_statistics.csv

Bio-Roary-3.0.2/t/data/empty_file

Bio-Roary-3.0.2/t/data/example_1.faa

Bio-Roary-3.0.2/t/data/example_2.faa

Bio-Roary-3.0.2/t/data/example_3.faa

Bio-Roary-3.0.2/t/data/example_annotation.gff

Bio-Roary-3.0.2/t/data/example_annotation.gff.proteome.faa.expected

Bio-Roary-3.0.2/t/data/example_annotation_2.gff

Bio-Roary-3.0.2/t/data/example_groups

Bio-Roary-3.0.2/t/data/example_groups_without_labels

Bio-Roary-3.0.2/t/data/exp_qc_report.csv

Bio-Roary-3.0.2/t/data/exp_qc_report_real.csv

Bio-Roary-3.0.2/t/data/expected_0.seq

Bio-Roary-3.0.2/t/data/expected_5.seq

Bio-Roary-3.0.2/t/data/expected_clustered_proteins

Bio-Roary-3.0.2/t/data/expected_clusters_to_inflate

Bio-Roary-3.0.2/t/data/expected_combined_proteome.fa

Bio-Roary-3.0.2/t/data/expected_combined_proteome_with_filtering.fa

Bio-Roary-3.0.2/t/data/expected_complement_of_groups.gg

Bio-Roary-3.0.2/t/data/expected_complement_of_groups_core0.66.gg

Bio-Roary-3.0.2/t/data/expected_core_gene_alignment.aln

Bio-Roary-3.0.2/t/data/expected_core_gene_alignment_core0.66.aln

Bio-Roary-3.0.2/t/data/expected_create_pan_genome.fa

Bio-Roary-3.0.2/t/data/expected_example_annotation_1.faa

Bio-Roary-3.0.2/t/data/expected_filtered_original_input.fa

Bio-Roary-3.0.2/t/data/expected_gff_set_difference_common_set_statistics.csv

Bio-Roary-3.0.2/t/data/expected_group_labels

Bio-Roary-3.0.2/t/data/expected_group_statitics.csv

Bio-Roary-3.0.2/t/data/expected_group_statitics_missing_genes.csv

Bio-Roary-3.0.2/t/data/expected_group_statitics_verbose.csv

Bio-Roary-3.0.2/t/data/expected_inflated_results

Bio-Roary-3.0.2/t/data/expected_intersection_of_groups.gg

Bio-Roary-3.0.2/t/data/expected_intersection_of_groups_core0.66.gg

Bio-Roary-3.0.2/t/data/expected_nnn_at_end.fa

Bio-Roary-3.0.2/t/data/expected_nuc_multifasta.fa.aln

Bio-Roary-3.0.2/t/data/expected_nuc_multifasta.faa

Bio-Roary-3.0.2/t/data/expected_number_of_conserved_genes.tab

Bio-Roary-3.0.2/t/data/expected_number_of_conserved_genes_0.6.tab

Bio-Roary-3.0.2/t/data/expected_number_of_genes_in_pan_genome.tab

Bio-Roary-3.0.2/t/data/expected_number_of_new_genes.tab

Bio-Roary-3.0.2/t/data/expected_number_of_unique_genes.tab

Bio-Roary-3.0.2/t/data/expected_out_of_order_fasta.fa.sorted.fa

Bio-Roary-3.0.2/t/data/expected_output_core_missing_genes.aln

Bio-Roary-3.0.2/t/data/expected_output_filtered.fa

Bio-Roary-3.0.2/t/data/expected_output_groups

Bio-Roary-3.0.2/t/data/expected_output_groups_cdhit

Bio-Roary-3.0.2/t/data/expected_output_groups_group_2.fa

Bio-Roary-3.0.2/t/data/expected_output_groups_group_2_multi.fa

Bio-Roary-3.0.2/t/data/expected_output_groups_group_5.fa

Bio-Roary-3.0.2/t/data/expected_output_groups_group_5_multi.fa

Bio-Roary-3.0.2/t/data/expected_output_merged.aln

Bio-Roary-3.0.2/t/data/expected_output_merged_sparse.aln

Bio-Roary-3.0.2/t/data/expected_pan_genome.fa

Bio-Roary-3.0.2/t/data/expected_pan_genome_one_gene_per_fasta.fa

Bio-Roary-3.0.2/t/data/expected_pan_genome_reference.fa

Bio-Roary-3.0.2/t/data/expected_prank_input.fa.aln

Bio-Roary-3.0.2/t/data/expected_query_1.fna

Bio-Roary-3.0.2/t/data/expected_query_2.fna

Bio-Roary-3.0.2/t/data/expected_reannotated_groups_file

Bio-Roary-3.0.2/t/data/expected_set_difference_common_set

Bio-Roary-3.0.2/t/data/expected_set_difference_common_set_plot.png

Bio-Roary-3.0.2/t/data/expected_set_difference_common_set_statistics.csv

Bio-Roary-3.0.2/t/data/expected_set_difference_unique_set_one

Bio-Roary-3.0.2/t/data/expected_set_difference_unique_set_one_statistics.csv

Bio-Roary-3.0.2/t/data/expected_set_difference_unique_set_two

Bio-Roary-3.0.2/t/data/expected_set_difference_unique_set_two_plot.png

Bio-Roary-3.0.2/t/data/expected_set_difference_unique_set_two_statistics.csv

Bio-Roary-3.0.2/t/data/expected_uneven_sequences.fa

Bio-Roary-3.0.2/t/data/expected_union_of_groups.gg

Bio-Roary-3.0.2/t/data/genbank_gbff/

Bio-Roary-3.0.2/t/data/group_1.fa.aln

Bio-Roary-3.0.2/t/data/group_9.fa

Bio-Roary-3.0.2/t/data/kraken_report.txt

Bio-Roary-3.0.2/t/data/kraken_test/

Bio-Roary-3.0.2/t/data/locus_tag_gffs/

Bio-Roary-3.0.2/t/data/mcl_file

Bio-Roary-3.0.2/t/data/mdoH.fa.aln

Bio-Roary-3.0.2/t/data/multfasta1.aln

Bio-Roary-3.0.2/t/data/multfasta2.aln

Bio-Roary-3.0.2/t/data/multfasta3.aln

Bio-Roary-3.0.2/t/data/multfasta4.aln

Bio-Roary-3.0.2/t/data/multfasta5.aln

Bio-Roary-3.0.2/t/data/nnn_at_end.fa

Bio-Roary-3.0.2/t/data/nnn_at_end.fa.sorted.fa

Bio-Roary-3.0.2/t/data/nuc_multifasta.fa

Bio-Roary-3.0.2/t/data/nuc_to_be_aligned.fa

Bio-Roary-3.0.2/t/data/out_of_order_fasta.fa

Bio-Roary-3.0.2/t/data/out_of_order_fasta.fa.sorted.fa

Bio-Roary-3.0.2/t/data/overall_gene_presence_absence.csv

Bio-Roary-3.0.2/t/data/pan_genome_sequences/

Bio-Roary-3.0.2/t/data/post_analysis/

Bio-Roary-3.0.2/t/data/post_analysis_expected/

Bio-Roary-3.0.2/t/data/prank_input.fa

Bio-Roary-3.0.2/t/data/proteome_with_and_without_descriptions.faa

Bio-Roary-3.0.2/t/data/query_1.fa

Bio-Roary-3.0.2/t/data/query_1.gff

Bio-Roary-3.0.2/t/data/query_1_alternative_patterns.gff

Bio-Roary-3.0.2/t/data/query_2.fa

Bio-Roary-3.0.2/t/data/query_2.gff

Bio-Roary-3.0.2/t/data/query_3.fa

Bio-Roary-3.0.2/t/data/query_3.gff

Bio-Roary-3.0.2/t/data/query_4_missing_genes.fa

Bio-Roary-3.0.2/t/data/query_4_missing_genes.gff

Bio-Roary-3.0.2/t/data/query_5.gff

Bio-Roary-3.0.2/t/data/query_6.gff

Bio-Roary-3.0.2/t/data/query_groups

Bio-Roary-3.0.2/t/data/query_groups_all_merged

Bio-Roary-3.0.2/t/data/query_groups_missing_genes

Bio-Roary-3.0.2/t/data/raxml.tre

Bio-Roary-3.0.2/t/data/real_data_1.gff

Bio-Roary-3.0.2/t/data/real_data_2.gff

Bio-Roary-3.0.2/t/data/real_data_core_gene_alignment.aln

Bio-Roary-3.0.2/t/data/reformat_input_gffs/

Bio-Roary-3.0.2/t/data/reorder_isolates.tre

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_breadth_alpha.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_breadth_creation.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_breadth_height.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_breadth_revalpha.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_depth_alpha.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_depth_creation.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_depth_height.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_depth_revalpha.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_input.csv

Bio-Roary-3.0.2/t/data/sequences_with_unknowns.faa

Bio-Roary-3.0.2/t/data/shred1.gff

Bio-Roary-3.0.2/t/data/shred1.shred.fa

Bio-Roary-3.0.2/t/data/shred2.gff

Bio-Roary-3.0.2/t/data/shred2.shred.fa

Bio-Roary-3.0.2/t/data/sopB.fa.aln

Bio-Roary-3.0.2/t/data/speH.fa.aln

Bio-Roary-3.0.2/t/data/split_groups/

Bio-Roary-3.0.2/t/data/split_pan_genome_sequences/

Bio-Roary-3.0.2/t/data/uneven_sequences.fa

Bio-Roary-3.0.2/t/data/uneven_sequences.fa.sorted.fa

Bio-Roary-3.0.2/t/data/variable_core/

Bio-Roary-3.0.2/t/data/variable_core/gene_1.fa.aln

Bio-Roary-3.0.2/t/data/variable_core/gene_2.fa.aln

Bio-Roary-3.0.2/t/data/variable_core/gene_3.fa.aln

Bio-Roary-3.0.2/t/data/variable_core/gene_4.fa.aln

Bio-Roary-3.0.2/t/data/variable_core/gene_5.fa.aln

Bio-Roary-3.0.2/t/data/split_pan_genome_sequences/argF.fa

Bio-Roary-3.0.2/t/data/split_pan_genome_sequences/different.fa

Bio-Roary-3.0.2/t/data/split_pan_genome_sequences/hly.fa

Bio-Roary-3.0.2/t/data/split_pan_genome_sequences/reannotated_groups_file

Bio-Roary-3.0.2/t/data/split_pan_genome_sequences/speH.fa

Bio-Roary-3.0.2/t/data/split_groups/paralog_clusters1

Bio-Roary-3.0.2/t/data/split_groups/paralog_clusters2

Bio-Roary-3.0.2/t/data/split_groups/paralog_clusters3

Bio-Roary-3.0.2/t/data/split_groups/paralog_clusters4

Bio-Roary-3.0.2/t/data/split_groups/paralog_exp_clusters1

Bio-Roary-3.0.2/t/data/split_groups/paralog_exp_clusters2

Bio-Roary-3.0.2/t/data/split_groups/paralog_exp_clusters3

Bio-Roary-3.0.2/t/data/split_groups/paralog_exp_clusters4

Bio-Roary-3.0.2/t/data/split_groups/paralogs1.fa

Bio-Roary-3.0.2/t/data/split_groups/paralogs2.fa

Bio-Roary-3.0.2/t/data/split_groups/paralogs3.fa

Bio-Roary-3.0.2/t/data/reformat_input_gffs/expected_fixed_query_2.gff

Bio-Roary-3.0.2/t/data/reformat_input_gffs/expected_fixed_query_3.gff

Bio-Roary-3.0.2/t/data/reformat_input_gffs/expected_real_1.gff

Bio-Roary-3.0.2/t/data/reformat_input_gffs/query_1.gff

Bio-Roary-3.0.2/t/data/reformat_input_gffs/query_2.gff

Bio-Roary-3.0.2/t/data/reformat_input_gffs/query_3.gff

Bio-Roary-3.0.2/t/data/reformat_input_gffs/real_1.gff

Bio-Roary-3.0.2/t/data/post_analysis_expected/accessory.header.embl

Bio-Roary-3.0.2/t/data/post_analysis_expected/accessory.tab

Bio-Roary-3.0.2/t/data/post_analysis_expected/core_accessory.header.embl

Bio-Roary-3.0.2/t/data/post_analysis_expected/core_accessory.tab

Bio-Roary-3.0.2/t/data/post_analysis_expected/gene_presence_absence.csv

Bio-Roary-3.0.2/t/data/post_analysis/_clustered

Bio-Roary-3.0.2/t/data/post_analysis/_clustered.bak.clstr

Bio-Roary-3.0.2/t/data/post_analysis/_clustered.clstr

Bio-Roary-3.0.2/t/data/post_analysis/_combined_files

Bio-Roary-3.0.2/t/data/post_analysis/_combined_files.groups

Bio-Roary-3.0.2/t/data/post_analysis/_fasta_files

Bio-Roary-3.0.2/t/data/post_analysis/_gff_files

Bio-Roary-3.0.2/t/data/post_analysis/_uninflated_mcl_groups

Bio-Roary-3.0.2/t/data/post_analysis/query_1.gff.proteome.faa

Bio-Roary-3.0.2/t/data/post_analysis/query_2.gff.proteome.faa

Bio-Roary-3.0.2/t/data/post_analysis/query_6.gff.proteome.faa

Bio-Roary-3.0.2/t/data/pan_genome_sequences/argF.fa

Bio-Roary-3.0.2/t/data/pan_genome_sequences/hly.fa

Bio-Roary-3.0.2/t/data/pan_genome_sequences/speH.fa

Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_1.gff

Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_1.gff.proteome.faa.expected

Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_2.gff

Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_2.gff.proteome.faa.expected

Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_3.gff

Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_3.gff.proteome.faa.expected

Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_5.gff

Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_5.gff.proteome.faa.expected

Bio-Roary-3.0.2/t/data/kraken_test/database.idx

Bio-Roary-3.0.2/t/data/kraken_test/database.jdb

Bio-Roary-3.0.2/t/data/kraken_test/database.kdb

Bio-Roary-3.0.2/t/data/kraken_test/taxonomy/

Bio-Roary-3.0.2/t/data/kraken_test/taxonomy/names.dmp

Bio-Roary-3.0.2/t/data/kraken_test/taxonomy/nodes.dmp

Bio-Roary-3.0.2/t/data/genbank_gbff/genbank1.gff

Bio-Roary-3.0.2/t/data/genbank_gbff/genbank1.gff.proteome.faa.expected

Bio-Roary-3.0.2/t/data/genbank_gbff/genbank2.gff

Bio-Roary-3.0.2/t/data/genbank_gbff/genbank2.gff.proteome.faa.expected

Bio-Roary-3.0.2/t/data/genbank_gbff/genbank3.gff

Bio-Roary-3.0.2/t/data/genbank_gbff/genbank3.gff.proteome.faa.expected

Bio-Roary-3.0.2/t/data/genbank_gbff/genbank_gene_presence_absence.csv

Bio-Roary-3.0.2/t/data/core_alignment/argF.fa.aln

Bio-Roary-3.0.2/t/data/core_alignment/hly.fa.aln

Bio-Roary-3.0.2/t/data/core_alignment/speH.fa.aln

Bio-Roary-3.0.2/t/data/accessory_graphs/core_deletion

Bio-Roary-3.0.2/t/data/accessory_graphs/core_island

Bio-Roary-3.0.2/t/data/accessory_graphs/file_1.fa

Bio-Roary-3.0.2/t/data/accessory_graphs/file_1.gff

Bio-Roary-3.0.2/t/data/accessory_graphs/file_2.fa

Bio-Roary-3.0.2/t/data/accessory_graphs/file_2.gff

Bio-Roary-3.0.2/t/data/accessory_graphs/file_3.fa

Bio-Roary-3.0.2/t/data/accessory_graphs/file_3.gff

Bio-Roary-3.0.2/t/data/accessory_graphs/no_accessory

Bio-Roary-3.0.2/t/data/accessory_graphs/one_branch

Bio-Roary-3.0.2/t/data/accessory_graphs/one_bubble

Bio-Roary-3.0.2/t/data/accessory_graphs/single_gene_contig

Bio-Roary-3.0.2/t/data/accessory_graphs/two_graphs

Bio-Roary-3.0.2/t/Bio/Roary/

Bio-Roary-3.0.2/t/Bio/Roary/AnalyseGroups.t

Bio-Roary-3.0.2/t/Bio/Roary/AnnotateGroups.t

Bio-Roary-3.0.2/t/Bio/Roary/ChunkFastaFile.t

Bio-Roary-3.0.2/t/Bio/Roary/CombinedProteome.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/

Bio-Roary-3.0.2/t/Bio/Roary/ContigsToGeneIDsFromGFF.t

Bio-Roary-3.0.2/t/Bio/Roary/External/

Bio-Roary-3.0.2/t/Bio/Roary/ExtractCoreGenesFromSpreadsheet.t

Bio-Roary-3.0.2/t/Bio/Roary/ExtractProteomeFromGFFs.t

Bio-Roary-3.0.2/t/Bio/Roary/FilterFullClusters.t

Bio-Roary-3.0.2/t/Bio/Roary/GeneNamesFromGFF.t

Bio-Roary-3.0.2/t/Bio/Roary/GroupLabels.t

Bio-Roary-3.0.2/t/Bio/Roary/GroupStatistics.t

Bio-Roary-3.0.2/t/Bio/Roary/InflateClusters.t

Bio-Roary-3.0.2/t/Bio/Roary/OrderGenes.t

Bio-Roary-3.0.2/t/Bio/Roary/Output/

Bio-Roary-3.0.2/t/Bio/Roary/ParallelAllAgainstAllBlast.t

Bio-Roary-3.0.2/t/Bio/Roary/PrepareInputFiles.t

Bio-Roary-3.0.2/t/Bio/Roary/QC/

Bio-Roary-3.0.2/t/Bio/Roary/ReformatInputGFFs.t

Bio-Roary-3.0.2/t/Bio/Roary/ReorderSpreadsheet.t

Bio-Roary-3.0.2/t/Bio/Roary/SampleOrder.t

Bio-Roary-3.0.2/t/Bio/Roary/SequenceLengths.t

Bio-Roary-3.0.2/t/Bio/Roary/SortFasta.t

Bio-Roary-3.0.2/t/Bio/Roary/SplitGroups.t

Bio-Roary-3.0.2/t/Bio/Roary/QC/Report.t

Bio-Roary-3.0.2/t/Bio/Roary/Output/DifferenceBetweenSets.t

Bio-Roary-3.0.2/t/Bio/Roary/Output/GroupsMultifastaProtein.t

Bio-Roary-3.0.2/t/Bio/Roary/Output/GroupsMultifastas.t

Bio-Roary-3.0.2/t/Bio/Roary/Output/GroupsMultifastasNucleotide.t

Bio-Roary-3.0.2/t/Bio/Roary/Output/NumberOfGroups.t

Bio-Roary-3.0.2/t/Bio/Roary/Output/QueryGroups.t

Bio-Roary-3.0.2/t/Bio/Roary/External/Blastp.t

Bio-Roary-3.0.2/t/Bio/Roary/External/Cdhit.t

Bio-Roary-3.0.2/t/Bio/Roary/External/Makeblastdb.t

Bio-Roary-3.0.2/t/Bio/Roary/External/Mcl.t

Bio-Roary-3.0.2/t/Bio/Roary/External/Prank.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/ExtractProteomeFromGff.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/QueryRoary.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/Roary.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/RoaryCoreAlignment.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/RoaryPostAnalysis.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/TransferAnnotationToGroups.t

Bio-Roary-3.0.2/t/bin/dummy_blastp

Bio-Roary-3.0.2/t/bin/dummy_cd-hit

Bio-Roary-3.0.2/t/bin/dummy_makeblastdb

Bio-Roary-3.0.2/t/bin/dummy_mcl

Bio-Roary-3.0.2/t/bin/dummy_mcxdeblast

Bio-Roary-3.0.2/t/bin/dummy_segmasker

Bio-Roary-3.0.2/lib/Bio/

Bio-Roary-3.0.2/lib/Bio/Roary/

Bio-Roary-3.0.2/lib/Bio/Roary.pm

Bio-Roary-3.0.2/lib/Bio/Roary/AnalyseGroups.pm

Bio-Roary-3.0.2/lib/Bio/Roary/AnnotateGroups.pm

Bio-Roary-3.0.2/lib/Bio/Roary/BedFromGFFRole.pm

Bio-Roary-3.0.2/lib/Bio/Roary/ChunkFastaFile.pm

Bio-Roary-3.0.2/lib/Bio/Roary/ClustersRole.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CombinedProteome.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/

Bio-Roary-3.0.2/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Exceptions.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/

Bio-Roary-3.0.2/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm

Bio-Roary-3.0.2/lib/Bio/Roary/ExtractProteomeFromGFF.pm

Bio-Roary-3.0.2/lib/Bio/Roary/ExtractProteomeFromGFFs.pm

Bio-Roary-3.0.2/lib/Bio/Roary/FilterFullClusters.pm

Bio-Roary-3.0.2/lib/Bio/Roary/FilterUnknownsFromFasta.pm

Bio-Roary-3.0.2/lib/Bio/Roary/GeneNamesFromGFF.pm

Bio-Roary-3.0.2/lib/Bio/Roary/GroupLabels.pm

Bio-Roary-3.0.2/lib/Bio/Roary/GroupStatistics.pm

Bio-Roary-3.0.2/lib/Bio/Roary/InflateClusters.pm

Bio-Roary-3.0.2/lib/Bio/Roary/IterativeCdhit.pm

Bio-Roary-3.0.2/lib/Bio/Roary/JobRunner/

Bio-Roary-3.0.2/lib/Bio/Roary/LookupGeneFiles.pm

Bio-Roary-3.0.2/lib/Bio/Roary/MergeMultifastaAlignments.pm

Bio-Roary-3.0.2/lib/Bio/Roary/OrderGenes.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/

Bio-Roary-3.0.2/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm

Bio-Roary-3.0.2/lib/Bio/Roary/ParseGFFAnnotationRole.pm

Bio-Roary-3.0.2/lib/Bio/Roary/PostAnalysis.pm

Bio-Roary-3.0.2/lib/Bio/Roary/PrepareInputFiles.pm

Bio-Roary-3.0.2/lib/Bio/Roary/QC/

Bio-Roary-3.0.2/lib/Bio/Roary/ReformatInputGFFs.pm

Bio-Roary-3.0.2/lib/Bio/Roary/ReorderSpreadsheet.pm

Bio-Roary-3.0.2/lib/Bio/Roary/SampleOrder.pm

Bio-Roary-3.0.2/lib/Bio/Roary/SequenceLengths.pm

Bio-Roary-3.0.2/lib/Bio/Roary/SortFasta.pm

Bio-Roary-3.0.2/lib/Bio/Roary/SplitGroups.pm

Bio-Roary-3.0.2/lib/Bio/Roary/QC/Report.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/BlastIdentityFrequency.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/DifferenceBetweenSets.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/EmblGroups.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/GroupMultifasta.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/GroupsMultifastas.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/NumberOfGroups.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/QueryGroups.pm

Bio-Roary-3.0.2/lib/Bio/Roary/JobRunner/Local.pm

Bio-Roary-3.0.2/lib/Bio/Roary/JobRunner/Parallel.pm

Bio-Roary-3.0.2/lib/Bio/Roary/JobRunner/Role.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/Blastp.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/Cdhit.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/IterativeCdhit.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/Makeblastdb.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/Mcl.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/PostAnalysis.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/Prank.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/ProteinMuscleAlignmentFromNucleotides.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/Common.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/CreatePanGenome.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/IterativeCdhit.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/QueryRoary.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/Roary.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm

Bio-Roary-3.0.2/contrib/roary_plots/

Bio-Roary-3.0.2/contrib/roary_plots/README.md

Bio-Roary-3.0.2/contrib/roary_plots/roary.html

Bio-Roary-3.0.2/contrib/roary_plots/roary_files/

Bio-Roary-3.0.2/contrib/roary_plots/roary_plots.ipynb

Bio-Roary-3.0.2/contrib/roary_plots/roary_plots.py

Bio-Roary-3.0.2/contrib/roary_plots/roary_files/jquery.min.js

Bio-Roary-3.0.2/contrib/roary_plots/roary_files/MathJax.js

Bio-Roary-3.0.2/contrib/roary_plots/roary_files/require.min.js

Bio-Roary-3.0.2/binaries/darwin/

Bio-Roary-3.0.2/binaries/linux/

Bio-Roary-3.0.2/binaries/linux/bedtools

Bio-Roary-3.0.2/binaries/linux/blastp

Bio-Roary-3.0.2/binaries/linux/cd-hit

Bio-Roary-3.0.2/binaries/linux/makeblastdb

Bio-Roary-3.0.2/binaries/linux/mcl

Bio-Roary-3.0.2/binaries/linux/mcxdeblast

Bio-Roary-3.0.2/binaries/linux/parallel

Bio-Roary-3.0.2/binaries/linux/prank

Bio-Roary-3.0.2/binaries/darwin/bedtools

Bio-Roary-3.0.2/binaries/darwin/blastp

Bio-Roary-3.0.2/binaries/darwin/cd-hit

Bio-Roary-3.0.2/binaries/darwin/makeblastdb

Bio-Roary-3.0.2/binaries/darwin/mcl

Bio-Roary-3.0.2/binaries/darwin/mcxdeblast

Bio-Roary-3.0.2/binaries/darwin/parallel

Bio-Roary-3.0.2/binaries/darwin/prank

Bio-Roary-3.0.2/bin/create_pan_genome

Bio-Roary-3.0.2/bin/create_pan_genome_plots.R

Bio-Roary-3.0.2/bin/extract_proteome_from_gff

Bio-Roary-3.0.2/bin/iterative_cdhit

Bio-Roary-3.0.2/bin/pan_genome_core_alignment

Bio-Roary-3.0.2/bin/pan_genome_post_analysis

Bio-Roary-3.0.2/bin/pan_genome_reorder_spreadsheet

Bio-Roary-3.0.2/bin/parallel_all_against_all_blastp

Bio-Roary-3.0.2/bin/protein_muscle_alignment_from_nucleotides

Bio-Roary-3.0.2/bin/query_pan_genome

Bio-Roary-3.0.2/bin/roary

Bio-Roary-3.0.2/bin/transfer_annotation_to_groups

Configuring Bio-Roary-3.0.2 ... Checking if your kit is complete...

Looks good

Generating a Unix-style Makefile

Writing Makefile for Bio::Roary

Writing MYMETA.yml and MYMETA.json

OK

Building and testing Bio-Roary-3.0.2 ... cp lib/Bio/Roary/External/IterativeCdhit.pm blib/lib/Bio/Roary/External/IterativeCdhit.pm

cp lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm blib/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm

cp lib/Bio/Roary/CommandLine/IterativeCdhit.pm blib/lib/Bio/Roary/CommandLine/IterativeCdhit.pm

cp lib/Bio/Roary.pm blib/lib/Bio/Roary.pm

cp lib/Bio/Roary/CommandLine/QueryRoary.pm blib/lib/Bio/Roary/CommandLine/QueryRoary.pm

cp lib/Bio/Roary/CombinedProteome.pm blib/lib/Bio/Roary/CombinedProteome.pm

cp lib/Bio/Roary/ChunkFastaFile.pm blib/lib/Bio/Roary/ChunkFastaFile.pm

cp lib/Bio/Roary/CommandLine/Roary.pm blib/lib/Bio/Roary/CommandLine/Roary.pm

cp lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm blib/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm

cp lib/Bio/Roary/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm

cp lib/Bio/Roary/Exceptions.pm blib/lib/Bio/Roary/Exceptions.pm

cp lib/Bio/Roary/External/Cdhit.pm blib/lib/Bio/Roary/External/Cdhit.pm

cp lib/Bio/Roary/CommandLine/Common.pm blib/lib/Bio/Roary/CommandLine/Common.pm

cp lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm blib/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm

cp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.pm

cp lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm

cp lib/Bio/Roary/External/Blastp.pm blib/lib/Bio/Roary/External/Blastp.pm

cp lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm

cp lib/Bio/Roary/External/Prank.pm blib/lib/Bio/Roary/External/Prank.pm

cp lib/Bio/Roary/CommandLine/CreatePanGenome.pm blib/lib/Bio/Roary/CommandLine/CreatePanGenome.pm

cp lib/Bio/Roary/ClustersRole.pm blib/lib/Bio/Roary/ClustersRole.pm

cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm

cp lib/Bio/Roary/AnnotateGroups.pm blib/lib/Bio/Roary/AnnotateGroups.pm

cp lib/Bio/Roary/External/Mcl.pm blib/lib/Bio/Roary/External/Mcl.pm

cp lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm blib/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm

cp lib/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.pm blib/lib/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.pm

cp lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm blib/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm

cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.pm

cp lib/Bio/Roary/External/ProteinMuscleAlignmentFromNucleotides.pm blib/lib/Bio/Roary/External/ProteinMuscleAlignmentFromNucleotides.pm

cp lib/Bio/Roary/External/Makeblastdb.pm blib/lib/Bio/Roary/External/Makeblastdb.pm

cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.pm

cp lib/Bio/Roary/GeneNamesFromGFF.pm blib/lib/Bio/Roary/GeneNamesFromGFF.pm

cp lib/Bio/Roary/ExtractProteomeFromGFF.pm blib/lib/Bio/Roary/ExtractProteomeFromGFF.pm

cp lib/Bio/Roary/JobRunner/Local.pm blib/lib/Bio/Roary/JobRunner/Local.pm

cp lib/Bio/Roary/Output/GroupsMultifastaProtein.pm blib/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm

cp lib/Bio/Roary/ExtractProteomeFromGFFs.pm blib/lib/Bio/Roary/ExtractProteomeFromGFFs.pm

cp lib/Bio/Roary/ReorderSpreadsheet.pm blib/lib/Bio/Roary/ReorderSpreadsheet.pm

cp lib/Bio/Roary/QC/Report.pm blib/lib/Bio/Roary/QC/Report.pm

cp lib/Bio/Roary/Output/EmblGroups.pm blib/lib/Bio/Roary/Output/EmblGroups.pm

cp lib/Bio/Roary/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm

cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm blib/lib/Bio/Roary/Output/DifferenceBetweenSets.pm

cp lib/Bio/Roary/Output/GroupsMultifastas.pm blib/lib/Bio/Roary/Output/GroupsMultifastas.pm

cp lib/Bio/Roary/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm

cp lib/Bio/Roary/Output/GroupMultifasta.pm blib/lib/Bio/Roary/Output/GroupMultifasta.pm

cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm

cp lib/Bio/Roary/Output/QueryGroups.pm blib/lib/Bio/Roary/Output/QueryGroups.pm

cp lib/Bio/Roary/Output/NumberOfGroups.pm blib/lib/Bio/Roary/Output/NumberOfGroups.pm

cp lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm

cp lib/Bio/Roary/GroupLabels.pm blib/lib/Bio/Roary/GroupLabels.pm

cp lib/Bio/Roary/JobRunner/Parallel.pm blib/lib/Bio/Roary/JobRunner/Parallel.pm

cp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm

cp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm

cp lib/Bio/Roary/FilterFullClusters.pm blib/lib/Bio/Roary/FilterFullClusters.pm

cp lib/Bio/Roary/MergeMultifastaAlignments.pm blib/lib/Bio/Roary/MergeMultifastaAlignments.pm

cp lib/Bio/Roary/PostAnalysis.pm blib/lib/Bio/Roary/PostAnalysis.pm

cp lib/Bio/Roary/PrepareInputFiles.pm blib/lib/Bio/Roary/PrepareInputFiles.pm

cp lib/Bio/Roary/Output/BlastIdentityFrequency.pm blib/lib/Bio/Roary/Output/BlastIdentityFrequency.pm

cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm

cp lib/Bio/Roary/JobRunner/Role.pm blib/lib/Bio/Roary/JobRunner/Role.pm

cp lib/Bio/Roary/InflateClusters.pm blib/lib/Bio/Roary/InflateClusters.pm

cp lib/Bio/Roary/OrderGenes.pm blib/lib/Bio/Roary/OrderGenes.pm

cp lib/Bio/Roary/FilterUnknownsFromFasta.pm blib/lib/Bio/Roary/FilterUnknownsFromFasta.pm

cp lib/Bio/Roary/SplitGroups.pm blib/lib/Bio/Roary/SplitGroups.pm

cp lib/Bio/Roary/SortFasta.pm blib/lib/Bio/Roary/SortFasta.pm

cp lib/Bio/Roary/SampleOrder.pm blib/lib/Bio/Roary/SampleOrder.pm

cp lib/Bio/Roary/SequenceLengths.pm blib/lib/Bio/Roary/SequenceLengths.pm

cp bin/pan_genome_reorder_spreadsheet blib/script/pan_genome_reorder_spreadsheet

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_reorder_spreadsheet

cp bin/iterative_cdhit blib/script/iterative_cdhit

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/iterative_cdhit

cp bin/create_pan_genome blib/script/create_pan_genome

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome

cp bin/query_pan_genome blib/script/query_pan_genome

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/query_pan_genome

cp bin/roary blib/script/roary

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary

cp bin/transfer_annotation_to_groups blib/script/transfer_annotation_to_groups

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/transfer_annotation_to_groups

cp bin/create_pan_genome_plots.R blib/script/create_pan_genome_plots.R

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome_plots.R

cp bin/pan_genome_post_analysis blib/script/pan_genome_post_analysis

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_post_analysis

cp bin/pan_genome_core_alignment blib/script/pan_genome_core_alignment

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_core_alignment

cp bin/parallel_all_against_all_blastp blib/script/parallel_all_against_all_blastp

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/parallel_all_against_all_blastp

cp bin/protein_muscle_alignment_from_nucleotides blib/script/protein_muscle_alignment_from_nucleotides

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/protein_muscle_alignment_from_nucleotides

cp bin/extract_proteome_from_gff blib/script/extract_proteome_from_gff

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/extract_proteome_from_gff

Manifying 12 pod documents

Manifying 26 pod documents

Manifying 26 pod documents

Manifying 14 pod documents

PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef _Test::Harness::Switches; testharness(0, 'blib/lib', 'blib/arch')" t/.t t/Bio/Roary/.t t/Bio/Roary/CommandLine/.t t/Bio/Roary/External/.t t/Bio/Roary/Output/.t t/Bio/Roary/QC/*.t

t/Bio/Roary/AnalyseGroups.t ...................................... ok

t/Bio/Roary/AnnotateGroups.t ..................................... ok

t/Bio/Roary/ChunkFastaFile.t ..................................... ok

t/Bio/Roary/CombinedProteome.t ................................... ok

t/Bio/Roary/CommandLine/ExtractProteomeFromGff.t ................. ok

t/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.t ............ ok

t/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.t .. ok

t/Bio/Roary/CommandLine/QueryRoary.t ............................. ok

t/Bio/Roary/CommandLine/Roary.t ..................................

Dubious, test returned 2 (wstat 512, 0x200)

Failed 1/9 subtests

t/Bio/Roary/CommandLine/RoaryCoreAlignment.t ..................... ok

t/Bio/Roary/CommandLine/RoaryPostAnalysis.t ...................... ok

t/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.t ................ ok

t/Bio/Roary/CommandLine/TransferAnnotationToGroups.t ............. ok

t/Bio/Roary/ContigsToGeneIDsFromGFF.t ............................ ok

t/Bio/Roary/External/Blastp.t .................................... ok

t/Bio/Roary/External/Cdhit.t ..................................... ok

t/Bio/Roary/External/Makeblastdb.t ............................... ok

t/Bio/Roary/External/Mcl.t ....................................... ok

t/Bio/Roary/External/Prank.t ..................................... ok

t/Bio/Roary/ExtractCoreGenesFromSpreadsheet.t .................... ok

t/Bio/Roary/ExtractProteomeFromGFFs.t ............................ ok

t/Bio/Roary/FilterFullClusters.t ................................. ok

t/Bio/Roary/GeneNamesFromGFF.t ................................... ok

t/Bio/Roary/GroupLabels.t ........................................ ok

t/Bio/Roary/GroupStatistics.t .................................... ok

t/Bio/Roary/InflateClusters.t .................................... ok

t/Bio/Roary/OrderGenes.t ......................................... ok

t/Bio/Roary/Output/DifferenceBetweenSets.t ....................... ok

t/Bio/Roary/Output/GroupsMultifastaProtein.t ..................... ok

t/Bio/Roary/Output/GroupsMultifastas.t ........................... ok

t/Bio/Roary/Output/GroupsMultifastasNucleotide.t ................. ok

t/Bio/Roary/Output/NumberOfGroups.t .............................. ok

t/Bio/Roary/Output/QueryGroups.t ................................. ok

t/Bio/Roary/ParallelAllAgainstAllBlast.t ......................... ok

t/Bio/Roary/PrepareInputFiles.t .................................. ok

t/Bio/Roary/QC/Report.t .......................................... ok

t/Bio/Roary/ReformatInputGFFs.t .................................. ok

t/Bio/Roary/ReorderSpreadsheet.t ................................. ok

t/Bio/Roary/SampleOrder.t ........................................ ok

t/Bio/Roary/SequenceLengths.t .................................... ok

t/Bio/Roary/SortFasta.t .......................................... ok

t/Bio/Roary/SplitGroups.t ........................................ ok

t/requires_external.t ............................................ ok

Test Summary Report

t/Bio/Roary/CommandLine/Roary.t (Wstat: 512 Tests: 9 Failed: 1)

Failed test: 9

Non-zero exit status: 2

Parse errors: No plan found in TAP output

Files=43, Tests=572, 70 wallclock secs ( 0.30 usr 0.08 sys + 62.44 cusr 7.66 csys = 70.48 CPU)

Result: FAIL

FAIL

Manifying 12 pod documents

Manifying 26 pod documents

Manifying 26 pod documents

Manifying 14 pod documents

Appending installation info to /usr/lib/perl/5.18/perllocal.pod

Successfully reinstalled Bio-Roary-3.0.2

Installing /usr/local/share/perl/5.18.2/x86_64-linux-gnu-thread-multi/.meta/Bio-Roary-3.0.2/install.json

1 distribution installed

— Reply to this email directly or view it on GitHub https://github.com/sanger-pathogens/Roary/issues/132#issuecomment-111863799 .

dutchscientist commented 9 years ago

Hi Andrew,

see below:

vanvlia@n85673:~/Roary$ perl t/Bio/Roary/CommandLine/Roary.t

ok 1 - use Bio::Roary::CommandLine::Roary;

ok 2 - use Bio::Roary::CommandLine::CreatePanGenome;

ok 3 - Actual output file exists gene_presence_absence.csv --dont_split_groups t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff

ok 4 - Actual and expected match output excluding variable columns

ok 5 - Actual output file exists gene_presence_absence.csv -j Local --dont_split_groups t/data/genbank_gbff/genbank1.gff t/data/genbank_gbff/genbank2.gff t/data/genbank_gbff/genbank3.gff

ok 6 - Actual and expected match output excluding variable columns

ok 7 - Actual output file exists gene_presence_absence.csv -j Local -t 1 --dont_split_groups t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff

ok 8 - Actual and expected match output excluding variable columns

parallel: Error: Command (--no-notice) starts with '-'. Is this a wrong option?

not ok 9 - Actual output file exists gene_presence_absence.csv -j Parallel --dont_split_groups t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff

Failed test 'Actual output file exists gene_presence_absence.csv -j Parallel --dont_split_groups t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff '

at t/lib/TestHelper.pm line 176.

Tests were run but no plan was declared and done_testing() was not seen.

Looks like your test exited with 2 just after 9.

andrewjpage commented 9 years ago

Thanks. It looks like its an issue with the parallel command. Could you send me the output of these commands?

which parallel parallel --version

Andrew

On 14 June 2015 at 20:16, dutchscientist notifications@github.com wrote:

Hi Andrew,

see below:

vanvlia@n85673:~/Roary$ perl t/Bio/Roary/CommandLine/Roary.t

ok 1 - use Bio::Roary::CommandLine::Roary;

ok 2 - use Bio::Roary::CommandLine::CreatePanGenome;

ok 3 - Actual output file exists gene_presence_absence.csv --dont_split_groups t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff

ok 4 - Actual and expected match output excluding variable columns

ok 5 - Actual output file exists gene_presence_absence.csv -j Local --dont_split_groups t/data/genbank_gbff/genbank1.gff t/data/genbank_gbff/genbank2.gff t/data/genbank_gbff/genbank3.gff

ok 6 - Actual and expected match output excluding variable columns

ok 7 - Actual output file exists gene_presence_absence.csv -j Local -t 1 --dont_split_groups t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff

ok 8 - Actual and expected match output excluding variable columns

parallel: Error: Command (--no-notice) starts with '-'. Is this a wrong option?

not ok 9 - Actual output file exists gene_presence_absence.csv -j Parallel --dont_split_groups t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff

Failed test 'Actual output file exists gene_presence_absence.csv -j

Parallel --dont_split_groups t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff '

at t/lib/TestHelper.pm line 176.

Tests were run but no plan was declared and done_testing() was not seen.

Looks like your test exited with 2 just after 9.

From: andrewjpage [mailto:notifications@github.com] Sent: 14 June 2015 20:00 To: sanger-pathogens/Roary Cc: dutchscientist Subject: Re: [Roary] Use of -e switch gives multifasta file with N's only (#132)

Thanks Arnoud for the output. I 'think' I know which tests is failing, but I was wondering if you could download the code and run the individual test which would give specific output? The commands are:

git clone https://github.com/sanger-pathogens/Roary.git cd Roary perl t/Bio/Roary/CommandLine/Roary.t

Thanks again for your time, your building up a lot of beer miles here!

On 14 June 2015 at 19:48, dutchscientist notifications@github.com wrote:

Hi Andrew,

this is the -v output.

--> Working on Bio::Roary

Fetching http://www.cpan.org/authors/id/A/AJ/AJPAGE/Bio-Roary-3.0.2.tar.gz ... OK

Bio-Roary-3.0.2/

Bio-Roary-3.0.2/AUTHORS

Bio-Roary-3.0.2/bin/

Bio-Roary-3.0.2/binaries/

Bio-Roary-3.0.2/contrib/

Bio-Roary-3.0.2/deployment_process

Bio-Roary-3.0.2/dist.ini

Bio-Roary-3.0.2/GPL-LICENSE

Bio-Roary-3.0.2/install_dependencies.sh

Bio-Roary-3.0.2/lib/

Bio-Roary-3.0.2/LICENSE

Bio-Roary-3.0.2/Makefile.PL

Bio-Roary-3.0.2/MANIFEST

Bio-Roary-3.0.2/META.yml

Bio-Roary-3.0.2/README

Bio-Roary-3.0.2/README.md

Bio-Roary-3.0.2/t/

Bio-Roary-3.0.2/t/bin/

Bio-Roary-3.0.2/t/Bio/

Bio-Roary-3.0.2/t/data/

Bio-Roary-3.0.2/t/dummy_blastp

Bio-Roary-3.0.2/t/dummy_cd-hit

Bio-Roary-3.0.2/t/dummy_makeblastdb

Bio-Roary-3.0.2/t/lib/

Bio-Roary-3.0.2/t/requires_external.t

Bio-Roary-3.0.2/t/lib/TestHelper.pm

Bio-Roary-3.0.2/t/data/accessory_graphs/

Bio-Roary-3.0.2/t/data/blast_results

Bio-Roary-3.0.2/t/data/clustered_proteins

Bio-Roary-3.0.2/t/data/clustered_proteins_pan_genome

Bio-Roary-3.0.2/t/data/clustered_proteins_post_analysis

Bio-Roary-3.0.2/t/data/clusters_input.fa

Bio-Roary-3.0.2/t/data/clusters_to_inflate

Bio-Roary-3.0.2/t/data/clusters_to_inflate.mcl

Bio-Roary-3.0.2/t/data/clusters_to_inflate_original_input.fa

Bio-Roary-3.0.2/t/data/clustersfile

Bio-Roary-3.0.2/t/data/core_alignment/

Bio-Roary-3.0.2/t/data/core_alignment.csv

Bio-Roary-3.0.2/t/data/core_alignment_core0.66.csv

Bio-Roary-3.0.2/t/data/core_group_statistics.csv

Bio-Roary-3.0.2/t/data/empty_file

Bio-Roary-3.0.2/t/data/example_1.faa

Bio-Roary-3.0.2/t/data/example_2.faa

Bio-Roary-3.0.2/t/data/example_3.faa

Bio-Roary-3.0.2/t/data/example_annotation.gff

Bio-Roary-3.0.2/t/data/example_annotation.gff.proteome.faa.expected

Bio-Roary-3.0.2/t/data/example_annotation_2.gff

Bio-Roary-3.0.2/t/data/example_groups

Bio-Roary-3.0.2/t/data/example_groups_without_labels

Bio-Roary-3.0.2/t/data/exp_qc_report.csv

Bio-Roary-3.0.2/t/data/exp_qc_report_real.csv

Bio-Roary-3.0.2/t/data/expected_0.seq

Bio-Roary-3.0.2/t/data/expected_5.seq

Bio-Roary-3.0.2/t/data/expected_clustered_proteins

Bio-Roary-3.0.2/t/data/expected_clusters_to_inflate

Bio-Roary-3.0.2/t/data/expected_combined_proteome.fa

Bio-Roary-3.0.2/t/data/expected_combined_proteome_with_filtering.fa

Bio-Roary-3.0.2/t/data/expected_complement_of_groups.gg

Bio-Roary-3.0.2/t/data/expected_complement_of_groups_core0.66.gg

Bio-Roary-3.0.2/t/data/expected_core_gene_alignment.aln

Bio-Roary-3.0.2/t/data/expected_core_gene_alignment_core0.66.aln

Bio-Roary-3.0.2/t/data/expected_create_pan_genome.fa

Bio-Roary-3.0.2/t/data/expected_example_annotation_1.faa

Bio-Roary-3.0.2/t/data/expected_filtered_original_input.fa

Bio-Roary-3.0.2/t/data/expected_gff_set_difference_common_set_statistics.csv

Bio-Roary-3.0.2/t/data/expected_group_labels

Bio-Roary-3.0.2/t/data/expected_group_statitics.csv

Bio-Roary-3.0.2/t/data/expected_group_statitics_missing_genes.csv

Bio-Roary-3.0.2/t/data/expected_group_statitics_verbose.csv

Bio-Roary-3.0.2/t/data/expected_inflated_results

Bio-Roary-3.0.2/t/data/expected_intersection_of_groups.gg

Bio-Roary-3.0.2/t/data/expected_intersection_of_groups_core0.66.gg

Bio-Roary-3.0.2/t/data/expected_nnn_at_end.fa

Bio-Roary-3.0.2/t/data/expected_nuc_multifasta.fa.aln

Bio-Roary-3.0.2/t/data/expected_nuc_multifasta.faa

Bio-Roary-3.0.2/t/data/expected_number_of_conserved_genes.tab

Bio-Roary-3.0.2/t/data/expected_number_of_conserved_genes_0.6.tab

Bio-Roary-3.0.2/t/data/expected_number_of_genes_in_pan_genome.tab

Bio-Roary-3.0.2/t/data/expected_number_of_new_genes.tab

Bio-Roary-3.0.2/t/data/expected_number_of_unique_genes.tab

Bio-Roary-3.0.2/t/data/expected_out_of_order_fasta.fa.sorted.fa

Bio-Roary-3.0.2/t/data/expected_output_core_missing_genes.aln

Bio-Roary-3.0.2/t/data/expected_output_filtered.fa

Bio-Roary-3.0.2/t/data/expected_output_groups

Bio-Roary-3.0.2/t/data/expected_output_groups_cdhit

Bio-Roary-3.0.2/t/data/expected_output_groups_group_2.fa

Bio-Roary-3.0.2/t/data/expected_output_groups_group_2_multi.fa

Bio-Roary-3.0.2/t/data/expected_output_groups_group_5.fa

Bio-Roary-3.0.2/t/data/expected_output_groups_group_5_multi.fa

Bio-Roary-3.0.2/t/data/expected_output_merged.aln

Bio-Roary-3.0.2/t/data/expected_output_merged_sparse.aln

Bio-Roary-3.0.2/t/data/expected_pan_genome.fa

Bio-Roary-3.0.2/t/data/expected_pan_genome_one_gene_per_fasta.fa

Bio-Roary-3.0.2/t/data/expected_pan_genome_reference.fa

Bio-Roary-3.0.2/t/data/expected_prank_input.fa.aln

Bio-Roary-3.0.2/t/data/expected_query_1.fna

Bio-Roary-3.0.2/t/data/expected_query_2.fna

Bio-Roary-3.0.2/t/data/expected_reannotated_groups_file

Bio-Roary-3.0.2/t/data/expected_set_difference_common_set

Bio-Roary-3.0.2/t/data/expected_set_difference_common_set_plot.png

Bio-Roary-3.0.2/t/data/expected_set_difference_common_set_statistics.csv

Bio-Roary-3.0.2/t/data/expected_set_difference_unique_set_one

Bio-Roary-3.0.2/t/data/expected_set_difference_unique_set_one_statistics.csv

Bio-Roary-3.0.2/t/data/expected_set_difference_unique_set_two

Bio-Roary-3.0.2/t/data/expected_set_difference_unique_set_two_plot.png

Bio-Roary-3.0.2/t/data/expected_set_difference_unique_set_two_statistics.csv

Bio-Roary-3.0.2/t/data/expected_uneven_sequences.fa

Bio-Roary-3.0.2/t/data/expected_union_of_groups.gg

Bio-Roary-3.0.2/t/data/genbank_gbff/

Bio-Roary-3.0.2/t/data/group_1.fa.aln

Bio-Roary-3.0.2/t/data/group_9.fa

Bio-Roary-3.0.2/t/data/kraken_report.txt

Bio-Roary-3.0.2/t/data/kraken_test/

Bio-Roary-3.0.2/t/data/locus_tag_gffs/

Bio-Roary-3.0.2/t/data/mcl_file

Bio-Roary-3.0.2/t/data/mdoH.fa.aln

Bio-Roary-3.0.2/t/data/multfasta1.aln

Bio-Roary-3.0.2/t/data/multfasta2.aln

Bio-Roary-3.0.2/t/data/multfasta3.aln

Bio-Roary-3.0.2/t/data/multfasta4.aln

Bio-Roary-3.0.2/t/data/multfasta5.aln

Bio-Roary-3.0.2/t/data/nnn_at_end.fa

Bio-Roary-3.0.2/t/data/nnn_at_end.fa.sorted.fa

Bio-Roary-3.0.2/t/data/nuc_multifasta.fa

Bio-Roary-3.0.2/t/data/nuc_to_be_aligned.fa

Bio-Roary-3.0.2/t/data/out_of_order_fasta.fa

Bio-Roary-3.0.2/t/data/out_of_order_fasta.fa.sorted.fa

Bio-Roary-3.0.2/t/data/overall_gene_presence_absence.csv

Bio-Roary-3.0.2/t/data/pan_genome_sequences/

Bio-Roary-3.0.2/t/data/post_analysis/

Bio-Roary-3.0.2/t/data/post_analysis_expected/

Bio-Roary-3.0.2/t/data/prank_input.fa

Bio-Roary-3.0.2/t/data/proteome_with_and_without_descriptions.faa

Bio-Roary-3.0.2/t/data/query_1.fa

Bio-Roary-3.0.2/t/data/query_1.gff

Bio-Roary-3.0.2/t/data/query_1_alternative_patterns.gff

Bio-Roary-3.0.2/t/data/query_2.fa

Bio-Roary-3.0.2/t/data/query_2.gff

Bio-Roary-3.0.2/t/data/query_3.fa

Bio-Roary-3.0.2/t/data/query_3.gff

Bio-Roary-3.0.2/t/data/query_4_missing_genes.fa

Bio-Roary-3.0.2/t/data/query_4_missing_genes.gff

Bio-Roary-3.0.2/t/data/query_5.gff

Bio-Roary-3.0.2/t/data/query_6.gff

Bio-Roary-3.0.2/t/data/query_groups

Bio-Roary-3.0.2/t/data/query_groups_all_merged

Bio-Roary-3.0.2/t/data/query_groups_missing_genes

Bio-Roary-3.0.2/t/data/raxml.tre

Bio-Roary-3.0.2/t/data/real_data_1.gff

Bio-Roary-3.0.2/t/data/real_data_2.gff

Bio-Roary-3.0.2/t/data/real_data_core_gene_alignment.aln

Bio-Roary-3.0.2/t/data/reformat_input_gffs/

Bio-Roary-3.0.2/t/data/reorder_isolates.tre

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_breadth_alpha.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_breadth_creation.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_breadth_height.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_breadth_revalpha.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_depth_alpha.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_depth_creation.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_depth_height.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_depth_revalpha.csv

Bio-Roary-3.0.2/t/data/reorder_isolates_input.csv

Bio-Roary-3.0.2/t/data/sequences_with_unknowns.faa

Bio-Roary-3.0.2/t/data/shred1.gff

Bio-Roary-3.0.2/t/data/shred1.shred.fa

Bio-Roary-3.0.2/t/data/shred2.gff

Bio-Roary-3.0.2/t/data/shred2.shred.fa

Bio-Roary-3.0.2/t/data/sopB.fa.aln

Bio-Roary-3.0.2/t/data/speH.fa.aln

Bio-Roary-3.0.2/t/data/split_groups/

Bio-Roary-3.0.2/t/data/split_pan_genome_sequences/

Bio-Roary-3.0.2/t/data/uneven_sequences.fa

Bio-Roary-3.0.2/t/data/uneven_sequences.fa.sorted.fa

Bio-Roary-3.0.2/t/data/variable_core/

Bio-Roary-3.0.2/t/data/variable_core/gene_1.fa.aln

Bio-Roary-3.0.2/t/data/variable_core/gene_2.fa.aln

Bio-Roary-3.0.2/t/data/variable_core/gene_3.fa.aln

Bio-Roary-3.0.2/t/data/variable_core/gene_4.fa.aln

Bio-Roary-3.0.2/t/data/variable_core/gene_5.fa.aln

Bio-Roary-3.0.2/t/data/split_pan_genome_sequences/argF.fa

Bio-Roary-3.0.2/t/data/split_pan_genome_sequences/different.fa

Bio-Roary-3.0.2/t/data/split_pan_genome_sequences/hly.fa

Bio-Roary-3.0.2/t/data/split_pan_genome_sequences/reannotated_groups_file

Bio-Roary-3.0.2/t/data/split_pan_genome_sequences/speH.fa

Bio-Roary-3.0.2/t/data/split_groups/paralog_clusters1

Bio-Roary-3.0.2/t/data/split_groups/paralog_clusters2

Bio-Roary-3.0.2/t/data/split_groups/paralog_clusters3

Bio-Roary-3.0.2/t/data/split_groups/paralog_clusters4

Bio-Roary-3.0.2/t/data/split_groups/paralog_exp_clusters1

Bio-Roary-3.0.2/t/data/split_groups/paralog_exp_clusters2

Bio-Roary-3.0.2/t/data/split_groups/paralog_exp_clusters3

Bio-Roary-3.0.2/t/data/split_groups/paralog_exp_clusters4

Bio-Roary-3.0.2/t/data/split_groups/paralogs1.fa

Bio-Roary-3.0.2/t/data/split_groups/paralogs2.fa

Bio-Roary-3.0.2/t/data/split_groups/paralogs3.fa

Bio-Roary-3.0.2/t/data/reformat_input_gffs/expected_fixed_query_2.gff

Bio-Roary-3.0.2/t/data/reformat_input_gffs/expected_fixed_query_3.gff

Bio-Roary-3.0.2/t/data/reformat_input_gffs/expected_real_1.gff

Bio-Roary-3.0.2/t/data/reformat_input_gffs/query_1.gff

Bio-Roary-3.0.2/t/data/reformat_input_gffs/query_2.gff

Bio-Roary-3.0.2/t/data/reformat_input_gffs/query_3.gff

Bio-Roary-3.0.2/t/data/reformat_input_gffs/real_1.gff

Bio-Roary-3.0.2/t/data/post_analysis_expected/accessory.header.embl

Bio-Roary-3.0.2/t/data/post_analysis_expected/accessory.tab

Bio-Roary-3.0.2/t/data/post_analysis_expected/core_accessory.header.embl

Bio-Roary-3.0.2/t/data/post_analysis_expected/core_accessory.tab

Bio-Roary-3.0.2/t/data/post_analysis_expected/gene_presence_absence.csv

Bio-Roary-3.0.2/t/data/post_analysis/_clustered

Bio-Roary-3.0.2/t/data/post_analysis/_clustered.bak.clstr

Bio-Roary-3.0.2/t/data/post_analysis/_clustered.clstr

Bio-Roary-3.0.2/t/data/post_analysis/_combined_files

Bio-Roary-3.0.2/t/data/post_analysis/_combined_files.groups

Bio-Roary-3.0.2/t/data/post_analysis/_fasta_files

Bio-Roary-3.0.2/t/data/post_analysis/_gff_files

Bio-Roary-3.0.2/t/data/post_analysis/_uninflated_mcl_groups

Bio-Roary-3.0.2/t/data/post_analysis/query_1.gff.proteome.faa

Bio-Roary-3.0.2/t/data/post_analysis/query_2.gff.proteome.faa

Bio-Roary-3.0.2/t/data/post_analysis/query_6.gff.proteome.faa

Bio-Roary-3.0.2/t/data/pan_genome_sequences/argF.fa

Bio-Roary-3.0.2/t/data/pan_genome_sequences/hly.fa

Bio-Roary-3.0.2/t/data/pan_genome_sequences/speH.fa

Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_1.gff

Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_1.gff.proteome.faa.expected

Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_2.gff

Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_2.gff.proteome.faa.expected

Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_3.gff

Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_3.gff.proteome.faa.expected

Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_5.gff

Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_5.gff.proteome.faa.expected

Bio-Roary-3.0.2/t/data/kraken_test/database.idx

Bio-Roary-3.0.2/t/data/kraken_test/database.jdb

Bio-Roary-3.0.2/t/data/kraken_test/database.kdb

Bio-Roary-3.0.2/t/data/kraken_test/taxonomy/

Bio-Roary-3.0.2/t/data/kraken_test/taxonomy/names.dmp

Bio-Roary-3.0.2/t/data/kraken_test/taxonomy/nodes.dmp

Bio-Roary-3.0.2/t/data/genbank_gbff/genbank1.gff

Bio-Roary-3.0.2/t/data/genbank_gbff/genbank1.gff.proteome.faa.expected

Bio-Roary-3.0.2/t/data/genbank_gbff/genbank2.gff

Bio-Roary-3.0.2/t/data/genbank_gbff/genbank2.gff.proteome.faa.expected

Bio-Roary-3.0.2/t/data/genbank_gbff/genbank3.gff

Bio-Roary-3.0.2/t/data/genbank_gbff/genbank3.gff.proteome.faa.expected

Bio-Roary-3.0.2/t/data/genbank_gbff/genbank_gene_presence_absence.csv

Bio-Roary-3.0.2/t/data/core_alignment/argF.fa.aln

Bio-Roary-3.0.2/t/data/core_alignment/hly.fa.aln

Bio-Roary-3.0.2/t/data/core_alignment/speH.fa.aln

Bio-Roary-3.0.2/t/data/accessory_graphs/core_deletion

Bio-Roary-3.0.2/t/data/accessory_graphs/core_island

Bio-Roary-3.0.2/t/data/accessory_graphs/file_1.fa

Bio-Roary-3.0.2/t/data/accessory_graphs/file_1.gff

Bio-Roary-3.0.2/t/data/accessory_graphs/file_2.fa

Bio-Roary-3.0.2/t/data/accessory_graphs/file_2.gff

Bio-Roary-3.0.2/t/data/accessory_graphs/file_3.fa

Bio-Roary-3.0.2/t/data/accessory_graphs/file_3.gff

Bio-Roary-3.0.2/t/data/accessory_graphs/no_accessory

Bio-Roary-3.0.2/t/data/accessory_graphs/one_branch

Bio-Roary-3.0.2/t/data/accessory_graphs/one_bubble

Bio-Roary-3.0.2/t/data/accessory_graphs/single_gene_contig

Bio-Roary-3.0.2/t/data/accessory_graphs/two_graphs

Bio-Roary-3.0.2/t/Bio/Roary/

Bio-Roary-3.0.2/t/Bio/Roary/AnalyseGroups.t

Bio-Roary-3.0.2/t/Bio/Roary/AnnotateGroups.t

Bio-Roary-3.0.2/t/Bio/Roary/ChunkFastaFile.t

Bio-Roary-3.0.2/t/Bio/Roary/CombinedProteome.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/

Bio-Roary-3.0.2/t/Bio/Roary/ContigsToGeneIDsFromGFF.t

Bio-Roary-3.0.2/t/Bio/Roary/External/

Bio-Roary-3.0.2/t/Bio/Roary/ExtractCoreGenesFromSpreadsheet.t

Bio-Roary-3.0.2/t/Bio/Roary/ExtractProteomeFromGFFs.t

Bio-Roary-3.0.2/t/Bio/Roary/FilterFullClusters.t

Bio-Roary-3.0.2/t/Bio/Roary/GeneNamesFromGFF.t

Bio-Roary-3.0.2/t/Bio/Roary/GroupLabels.t

Bio-Roary-3.0.2/t/Bio/Roary/GroupStatistics.t

Bio-Roary-3.0.2/t/Bio/Roary/InflateClusters.t

Bio-Roary-3.0.2/t/Bio/Roary/OrderGenes.t

Bio-Roary-3.0.2/t/Bio/Roary/Output/

Bio-Roary-3.0.2/t/Bio/Roary/ParallelAllAgainstAllBlast.t

Bio-Roary-3.0.2/t/Bio/Roary/PrepareInputFiles.t

Bio-Roary-3.0.2/t/Bio/Roary/QC/

Bio-Roary-3.0.2/t/Bio/Roary/ReformatInputGFFs.t

Bio-Roary-3.0.2/t/Bio/Roary/ReorderSpreadsheet.t

Bio-Roary-3.0.2/t/Bio/Roary/SampleOrder.t

Bio-Roary-3.0.2/t/Bio/Roary/SequenceLengths.t

Bio-Roary-3.0.2/t/Bio/Roary/SortFasta.t

Bio-Roary-3.0.2/t/Bio/Roary/SplitGroups.t

Bio-Roary-3.0.2/t/Bio/Roary/QC/Report.t

Bio-Roary-3.0.2/t/Bio/Roary/Output/DifferenceBetweenSets.t

Bio-Roary-3.0.2/t/Bio/Roary/Output/GroupsMultifastaProtein.t

Bio-Roary-3.0.2/t/Bio/Roary/Output/GroupsMultifastas.t

Bio-Roary-3.0.2/t/Bio/Roary/Output/GroupsMultifastasNucleotide.t

Bio-Roary-3.0.2/t/Bio/Roary/Output/NumberOfGroups.t

Bio-Roary-3.0.2/t/Bio/Roary/Output/QueryGroups.t

Bio-Roary-3.0.2/t/Bio/Roary/External/Blastp.t

Bio-Roary-3.0.2/t/Bio/Roary/External/Cdhit.t

Bio-Roary-3.0.2/t/Bio/Roary/External/Makeblastdb.t

Bio-Roary-3.0.2/t/Bio/Roary/External/Mcl.t

Bio-Roary-3.0.2/t/Bio/Roary/External/Prank.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/ExtractProteomeFromGff.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/QueryRoary.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/Roary.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/RoaryCoreAlignment.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/RoaryPostAnalysis.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.t

Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/TransferAnnotationToGroups.t

Bio-Roary-3.0.2/t/bin/dummy_blastp

Bio-Roary-3.0.2/t/bin/dummy_cd-hit

Bio-Roary-3.0.2/t/bin/dummy_makeblastdb

Bio-Roary-3.0.2/t/bin/dummy_mcl

Bio-Roary-3.0.2/t/bin/dummy_mcxdeblast

Bio-Roary-3.0.2/t/bin/dummy_segmasker

Bio-Roary-3.0.2/lib/Bio/

Bio-Roary-3.0.2/lib/Bio/Roary/

Bio-Roary-3.0.2/lib/Bio/Roary.pm

Bio-Roary-3.0.2/lib/Bio/Roary/AnalyseGroups.pm

Bio-Roary-3.0.2/lib/Bio/Roary/AnnotateGroups.pm

Bio-Roary-3.0.2/lib/Bio/Roary/BedFromGFFRole.pm

Bio-Roary-3.0.2/lib/Bio/Roary/ChunkFastaFile.pm

Bio-Roary-3.0.2/lib/Bio/Roary/ClustersRole.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CombinedProteome.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/

Bio-Roary-3.0.2/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Exceptions.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/

Bio-Roary-3.0.2/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm

Bio-Roary-3.0.2/lib/Bio/Roary/ExtractProteomeFromGFF.pm

Bio-Roary-3.0.2/lib/Bio/Roary/ExtractProteomeFromGFFs.pm

Bio-Roary-3.0.2/lib/Bio/Roary/FilterFullClusters.pm

Bio-Roary-3.0.2/lib/Bio/Roary/FilterUnknownsFromFasta.pm

Bio-Roary-3.0.2/lib/Bio/Roary/GeneNamesFromGFF.pm

Bio-Roary-3.0.2/lib/Bio/Roary/GroupLabels.pm

Bio-Roary-3.0.2/lib/Bio/Roary/GroupStatistics.pm

Bio-Roary-3.0.2/lib/Bio/Roary/InflateClusters.pm

Bio-Roary-3.0.2/lib/Bio/Roary/IterativeCdhit.pm

Bio-Roary-3.0.2/lib/Bio/Roary/JobRunner/

Bio-Roary-3.0.2/lib/Bio/Roary/LookupGeneFiles.pm

Bio-Roary-3.0.2/lib/Bio/Roary/MergeMultifastaAlignments.pm

Bio-Roary-3.0.2/lib/Bio/Roary/OrderGenes.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/

Bio-Roary-3.0.2/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm

Bio-Roary-3.0.2/lib/Bio/Roary/ParseGFFAnnotationRole.pm

Bio-Roary-3.0.2/lib/Bio/Roary/PostAnalysis.pm

Bio-Roary-3.0.2/lib/Bio/Roary/PrepareInputFiles.pm

Bio-Roary-3.0.2/lib/Bio/Roary/QC/

Bio-Roary-3.0.2/lib/Bio/Roary/ReformatInputGFFs.pm

Bio-Roary-3.0.2/lib/Bio/Roary/ReorderSpreadsheet.pm

Bio-Roary-3.0.2/lib/Bio/Roary/SampleOrder.pm

Bio-Roary-3.0.2/lib/Bio/Roary/SequenceLengths.pm

Bio-Roary-3.0.2/lib/Bio/Roary/SortFasta.pm

Bio-Roary-3.0.2/lib/Bio/Roary/SplitGroups.pm

Bio-Roary-3.0.2/lib/Bio/Roary/QC/Report.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/BlastIdentityFrequency.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/DifferenceBetweenSets.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/EmblGroups.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/GroupMultifasta.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/GroupsMultifastas.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/NumberOfGroups.pm

Bio-Roary-3.0.2/lib/Bio/Roary/Output/QueryGroups.pm

Bio-Roary-3.0.2/lib/Bio/Roary/JobRunner/Local.pm

Bio-Roary-3.0.2/lib/Bio/Roary/JobRunner/Parallel.pm

Bio-Roary-3.0.2/lib/Bio/Roary/JobRunner/Role.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/Blastp.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/Cdhit.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/IterativeCdhit.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/Makeblastdb.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/Mcl.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/PostAnalysis.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/Prank.pm

Bio-Roary-3.0.2/lib/Bio/Roary/External/ProteinMuscleAlignmentFromNucleotides.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/Common.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/CreatePanGenome.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/IterativeCdhit.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/QueryRoary.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/Roary.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm

Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm

Bio-Roary-3.0.2/contrib/roary_plots/

Bio-Roary-3.0.2/contrib/roary_plots/README.md

Bio-Roary-3.0.2/contrib/roary_plots/roary.html

Bio-Roary-3.0.2/contrib/roary_plots/roary_files/

Bio-Roary-3.0.2/contrib/roary_plots/roary_plots.ipynb

Bio-Roary-3.0.2/contrib/roary_plots/roary_plots.py

Bio-Roary-3.0.2/contrib/roary_plots/roary_files/jquery.min.js

Bio-Roary-3.0.2/contrib/roary_plots/roary_files/MathJax.js

Bio-Roary-3.0.2/contrib/roary_plots/roary_files/require.min.js

Bio-Roary-3.0.2/binaries/darwin/

Bio-Roary-3.0.2/binaries/linux/

Bio-Roary-3.0.2/binaries/linux/bedtools

Bio-Roary-3.0.2/binaries/linux/blastp

Bio-Roary-3.0.2/binaries/linux/cd-hit

Bio-Roary-3.0.2/binaries/linux/makeblastdb

Bio-Roary-3.0.2/binaries/linux/mcl

Bio-Roary-3.0.2/binaries/linux/mcxdeblast

Bio-Roary-3.0.2/binaries/linux/parallel

Bio-Roary-3.0.2/binaries/linux/prank

Bio-Roary-3.0.2/binaries/darwin/bedtools

Bio-Roary-3.0.2/binaries/darwin/blastp

Bio-Roary-3.0.2/binaries/darwin/cd-hit

Bio-Roary-3.0.2/binaries/darwin/makeblastdb

Bio-Roary-3.0.2/binaries/darwin/mcl

Bio-Roary-3.0.2/binaries/darwin/mcxdeblast

Bio-Roary-3.0.2/binaries/darwin/parallel

Bio-Roary-3.0.2/binaries/darwin/prank

Bio-Roary-3.0.2/bin/create_pan_genome

Bio-Roary-3.0.2/bin/create_pan_genome_plots.R

Bio-Roary-3.0.2/bin/extract_proteome_from_gff

Bio-Roary-3.0.2/bin/iterative_cdhit

Bio-Roary-3.0.2/bin/pan_genome_core_alignment

Bio-Roary-3.0.2/bin/pan_genome_post_analysis

Bio-Roary-3.0.2/bin/pan_genome_reorder_spreadsheet

Bio-Roary-3.0.2/bin/parallel_all_against_all_blastp

Bio-Roary-3.0.2/bin/protein_muscle_alignment_from_nucleotides

Bio-Roary-3.0.2/bin/query_pan_genome

Bio-Roary-3.0.2/bin/roary

Bio-Roary-3.0.2/bin/transfer_annotation_to_groups

Configuring Bio-Roary-3.0.2 ... Checking if your kit is complete...

Looks good

Generating a Unix-style Makefile

Writing Makefile for Bio::Roary

Writing MYMETA.yml and MYMETA.json

OK

Building and testing Bio-Roary-3.0.2 ... cp lib/Bio/Roary/External/IterativeCdhit.pm blib/lib/Bio/Roary/External/IterativeCdhit.pm

cp lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm blib/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm

cp lib/Bio/Roary/CommandLine/IterativeCdhit.pm blib/lib/Bio/Roary/CommandLine/IterativeCdhit.pm

cp lib/Bio/Roary.pm blib/lib/Bio/Roary.pm

cp lib/Bio/Roary/CommandLine/QueryRoary.pm blib/lib/Bio/Roary/CommandLine/QueryRoary.pm

cp lib/Bio/Roary/CombinedProteome.pm blib/lib/Bio/Roary/CombinedProteome.pm

cp lib/Bio/Roary/ChunkFastaFile.pm blib/lib/Bio/Roary/ChunkFastaFile.pm

cp lib/Bio/Roary/CommandLine/Roary.pm blib/lib/Bio/Roary/CommandLine/Roary.pm

cp lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm blib/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm

cp lib/Bio/Roary/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm

cp lib/Bio/Roary/Exceptions.pm blib/lib/Bio/Roary/Exceptions.pm

cp lib/Bio/Roary/External/Cdhit.pm blib/lib/Bio/Roary/External/Cdhit.pm

cp lib/Bio/Roary/CommandLine/Common.pm blib/lib/Bio/Roary/CommandLine/Common.pm

cp lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm blib/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm

cp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.pm

cp lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm

cp lib/Bio/Roary/External/Blastp.pm blib/lib/Bio/Roary/External/Blastp.pm

cp lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm

cp lib/Bio/Roary/External/Prank.pm blib/lib/Bio/Roary/External/Prank.pm

cp lib/Bio/Roary/CommandLine/CreatePanGenome.pm blib/lib/Bio/Roary/CommandLine/CreatePanGenome.pm

cp lib/Bio/Roary/ClustersRole.pm blib/lib/Bio/Roary/ClustersRole.pm

cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm

cp lib/Bio/Roary/AnnotateGroups.pm blib/lib/Bio/Roary/AnnotateGroups.pm

cp lib/Bio/Roary/External/Mcl.pm blib/lib/Bio/Roary/External/Mcl.pm

cp lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm blib/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm

cp lib/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.pm blib/lib/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.pm

cp lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm blib/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm

cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.pm

cp lib/Bio/Roary/External/ProteinMuscleAlignmentFromNucleotides.pm blib/lib/Bio/Roary/External/ProteinMuscleAlignmentFromNucleotides.pm

cp lib/Bio/Roary/External/Makeblastdb.pm blib/lib/Bio/Roary/External/Makeblastdb.pm

cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.pm

cp lib/Bio/Roary/GeneNamesFromGFF.pm blib/lib/Bio/Roary/GeneNamesFromGFF.pm

cp lib/Bio/Roary/ExtractProteomeFromGFF.pm blib/lib/Bio/Roary/ExtractProteomeFromGFF.pm

cp lib/Bio/Roary/JobRunner/Local.pm blib/lib/Bio/Roary/JobRunner/Local.pm

cp lib/Bio/Roary/Output/GroupsMultifastaProtein.pm blib/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm

cp lib/Bio/Roary/ExtractProteomeFromGFFs.pm blib/lib/Bio/Roary/ExtractProteomeFromGFFs.pm

cp lib/Bio/Roary/ReorderSpreadsheet.pm blib/lib/Bio/Roary/ReorderSpreadsheet.pm

cp lib/Bio/Roary/QC/Report.pm blib/lib/Bio/Roary/QC/Report.pm

cp lib/Bio/Roary/Output/EmblGroups.pm blib/lib/Bio/Roary/Output/EmblGroups.pm

cp lib/Bio/Roary/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm

cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm blib/lib/Bio/Roary/Output/DifferenceBetweenSets.pm

cp lib/Bio/Roary/Output/GroupsMultifastas.pm blib/lib/Bio/Roary/Output/GroupsMultifastas.pm

cp lib/Bio/Roary/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm

cp lib/Bio/Roary/Output/GroupMultifasta.pm blib/lib/Bio/Roary/Output/GroupMultifasta.pm

cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm

cp lib/Bio/Roary/Output/QueryGroups.pm blib/lib/Bio/Roary/Output/QueryGroups.pm

cp lib/Bio/Roary/Output/NumberOfGroups.pm blib/lib/Bio/Roary/Output/NumberOfGroups.pm

cp lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm

cp lib/Bio/Roary/GroupLabels.pm blib/lib/Bio/Roary/GroupLabels.pm

cp lib/Bio/Roary/JobRunner/Parallel.pm blib/lib/Bio/Roary/JobRunner/Parallel.pm

cp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm

cp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm

cp lib/Bio/Roary/FilterFullClusters.pm blib/lib/Bio/Roary/FilterFullClusters.pm

cp lib/Bio/Roary/MergeMultifastaAlignments.pm blib/lib/Bio/Roary/MergeMultifastaAlignments.pm

cp lib/Bio/Roary/PostAnalysis.pm blib/lib/Bio/Roary/PostAnalysis.pm

cp lib/Bio/Roary/PrepareInputFiles.pm blib/lib/Bio/Roary/PrepareInputFiles.pm

cp lib/Bio/Roary/Output/BlastIdentityFrequency.pm blib/lib/Bio/Roary/Output/BlastIdentityFrequency.pm

cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm

cp lib/Bio/Roary/JobRunner/Role.pm blib/lib/Bio/Roary/JobRunner/Role.pm

cp lib/Bio/Roary/InflateClusters.pm blib/lib/Bio/Roary/InflateClusters.pm

cp lib/Bio/Roary/OrderGenes.pm blib/lib/Bio/Roary/OrderGenes.pm

cp lib/Bio/Roary/FilterUnknownsFromFasta.pm blib/lib/Bio/Roary/FilterUnknownsFromFasta.pm

cp lib/Bio/Roary/SplitGroups.pm blib/lib/Bio/Roary/SplitGroups.pm

cp lib/Bio/Roary/SortFasta.pm blib/lib/Bio/Roary/SortFasta.pm

cp lib/Bio/Roary/SampleOrder.pm blib/lib/Bio/Roary/SampleOrder.pm

cp lib/Bio/Roary/SequenceLengths.pm blib/lib/Bio/Roary/SequenceLengths.pm

cp bin/pan_genome_reorder_spreadsheet blib/script/pan_genome_reorder_spreadsheet

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_reorder_spreadsheet

cp bin/iterative_cdhit blib/script/iterative_cdhit

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/iterative_cdhit

cp bin/create_pan_genome blib/script/create_pan_genome

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome

cp bin/query_pan_genome blib/script/query_pan_genome

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/query_pan_genome

cp bin/roary blib/script/roary

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary

cp bin/transfer_annotation_to_groups blib/script/transfer_annotation_to_groups

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/transfer_annotation_to_groups

cp bin/create_pan_genome_plots.R blib/script/create_pan_genome_plots.R

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome_plots.R

cp bin/pan_genome_post_analysis blib/script/pan_genome_post_analysis

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_post_analysis

cp bin/pan_genome_core_alignment blib/script/pan_genome_core_alignment

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_core_alignment

cp bin/parallel_all_against_all_blastp blib/script/parallel_all_against_all_blastp

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/parallel_all_against_all_blastp

cp bin/protein_muscle_alignment_from_nucleotides blib/script/protein_muscle_alignment_from_nucleotides

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/protein_muscle_alignment_from_nucleotides

cp bin/extract_proteome_from_gff blib/script/extract_proteome_from_gff

"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/extract_proteome_from_gff

Manifying 12 pod documents

Manifying 26 pod documents

Manifying 26 pod documents

Manifying 14 pod documents

PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef _Test::Harness::Switches; testharness(0, 'blib/lib', 'blib/arch')" t/.t t/Bio/Roary/.t t/Bio/Roary/CommandLine/.t t/Bio/Roary/External/.t t/Bio/Roary/Output/.t t/Bio/Roary/QC/*.t

t/Bio/Roary/AnalyseGroups.t ...................................... ok

t/Bio/Roary/AnnotateGroups.t ..................................... ok

t/Bio/Roary/ChunkFastaFile.t ..................................... ok

t/Bio/Roary/CombinedProteome.t ................................... ok

t/Bio/Roary/CommandLine/ExtractProteomeFromGff.t ................. ok

t/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.t ............ ok

t/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.t .. ok

t/Bio/Roary/CommandLine/QueryRoary.t ............................. ok

t/Bio/Roary/CommandLine/Roary.t ..................................

Dubious, test returned 2 (wstat 512, 0x200)

Failed 1/9 subtests

t/Bio/Roary/CommandLine/RoaryCoreAlignment.t ..................... ok

t/Bio/Roary/CommandLine/RoaryPostAnalysis.t ...................... ok

t/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.t ................ ok

t/Bio/Roary/CommandLine/TransferAnnotationToGroups.t ............. ok

t/Bio/Roary/ContigsToGeneIDsFromGFF.t ............................ ok

t/Bio/Roary/External/Blastp.t .................................... ok

t/Bio/Roary/External/Cdhit.t ..................................... ok

t/Bio/Roary/External/Makeblastdb.t ............................... ok

t/Bio/Roary/External/Mcl.t ....................................... ok

t/Bio/Roary/External/Prank.t ..................................... ok

t/Bio/Roary/ExtractCoreGenesFromSpreadsheet.t .................... ok

t/Bio/Roary/ExtractProteomeFromGFFs.t ............................ ok

t/Bio/Roary/FilterFullClusters.t ................................. ok

t/Bio/Roary/GeneNamesFromGFF.t ................................... ok

t/Bio/Roary/GroupLabels.t ........................................ ok

t/Bio/Roary/GroupStatistics.t .................................... ok

t/Bio/Roary/InflateClusters.t .................................... ok

t/Bio/Roary/OrderGenes.t ......................................... ok

t/Bio/Roary/Output/DifferenceBetweenSets.t ....................... ok

t/Bio/Roary/Output/GroupsMultifastaProtein.t ..................... ok

t/Bio/Roary/Output/GroupsMultifastas.t ........................... ok

t/Bio/Roary/Output/GroupsMultifastasNucleotide.t ................. ok

t/Bio/Roary/Output/NumberOfGroups.t .............................. ok

t/Bio/Roary/Output/QueryGroups.t ................................. ok

t/Bio/Roary/ParallelAllAgainstAllBlast.t ......................... ok

t/Bio/Roary/PrepareInputFiles.t .................................. ok

t/Bio/Roary/QC/Report.t .......................................... ok

t/Bio/Roary/ReformatInputGFFs.t .................................. ok

t/Bio/Roary/ReorderSpreadsheet.t ................................. ok

t/Bio/Roary/SampleOrder.t ........................................ ok

t/Bio/Roary/SequenceLengths.t .................................... ok

t/Bio/Roary/SortFasta.t .......................................... ok

t/Bio/Roary/SplitGroups.t ........................................ ok

t/requires_external.t ............................................ ok

Test Summary Report

t/Bio/Roary/CommandLine/Roary.t (Wstat: 512 Tests: 9 Failed: 1)

Failed test: 9

Non-zero exit status: 2

Parse errors: No plan found in TAP output

Files=43, Tests=572, 70 wallclock secs ( 0.30 usr 0.08 sys + 62.44 cusr 7.66 csys = 70.48 CPU)

Result: FAIL

FAIL

Manifying 12 pod documents

Manifying 26 pod documents

Manifying 26 pod documents

Manifying 14 pod documents

Appending installation info to /usr/lib/perl/5.18/perllocal.pod

Successfully reinstalled Bio-Roary-3.0.2

Installing

/usr/local/share/perl/5.18.2/x86_64-linux-gnu-thread-multi/.meta/Bio-Roary-3.0.2/install.json

1 distribution installed

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dutchscientist commented 9 years ago

vanvlia@n85673:~/data/listeria$ which parallel /usr/local/bin/parallel vanvlia@n85673:~/data/listeria$ parallel --version GNU parallel 20130422

I use this version of parallel as this is required for Prokka.

andrewjpage commented 9 years ago

Thanks.

On 14 June 2015 at 20:38, dutchscientist notifications@github.com wrote:

vanvlia@n85673:~/data/listeria$ which parallel /usr/local/bin/parallel vanvlia@n85673:~/data/listeria$ parallel --version GNU parallel 20130422

I use this version of parallel as this is required for Prokka.

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dutchscientist commented 9 years ago

I will check with Torsten Seemann how much flexibility there is with the Parallel version. I assume it won't be possible to run multiple versions.

andrewjpage commented 9 years ago

I've got a test setup on TravisCI with parallel versions 20130922, 20141022 and 20150522 so something else must be up. From looking at your data I think I know what might be up, but it will be tomorrow before I can confirm it.

On 14 June 2015 at 21:38, dutchscientist notifications@github.com wrote:

I will check with Torsten Seemann how much flexibility there is with the Parallel version. I assume it won't be possible to run multiple versions.

— Reply to this email directly or view it on GitHub https://github.com/sanger-pathogens/Roary/issues/132#issuecomment-111874757 .

dutchscientist commented 9 years ago

OK, very happy to do more tests, just remember, I am not a Linux expert. The instructions given were very helpful, that level I can do! ;-)

andrewjpage commented 9 years ago

Hi Arnoud, I've tracked down the problem and fixed it. The latest version is 3.0.3. The parallel warning messages seem to be a bit of a red herring. Give it a whirl and let me know how you get along. I've attached the core gene alignment for your campy data. Thanks for all the helpful feedback and for your patience. If your ever over Cambridge direction, I'll buy you a pint or two. Andrew

On 14 June 2015 at 22:10, dutchscientist notifications@github.com wrote:

OK, very happy to do more tests, just remember, I am not a Linux expert. The instructions given were very helpful, that level I can do! ;-)

— Reply to this email directly or view it on GitHub https://github.com/sanger-pathogens/Roary/issues/132#issuecomment-111876254 .

dutchscientist commented 9 years ago

Hi Andrew,

CPAN still has 3.0.2 on it, while the website has 3.0.3? The "sudo cpanm -f Bio::Roary" command gives 3.0.2 (I have done sudo apt-get update).

Beers are always a good idea!

From: andrewjpage [mailto:notifications@github.com] Sent: 15 June 2015 14:42 To: sanger-pathogens/Roary Cc: dutchscientist Subject: Re: [Roary] Use of -e switch gives multifasta file with N's only (#132)

Hi Arnoud, I've tracked down the problem and fixed it. The latest version is 3.0.3. The parallel warning messages seem to be a bit of a red herring. Give it a whirl and let me know how you get along. I've attached the core gene alignment for your campy data. Thanks for all the helpful feedback and for your patience. If your ever over Cambridge direction, I'll buy you a pint or two. Andrew

On 14 June 2015 at 22:10, dutchscientist notifications@github.com wrote:

OK, very happy to do more tests, just remember, I am not a Linux expert. The instructions given were very helpful, that level I can do! ;-)

— Reply to this email directly or view it on GitHub https://github.com/sanger-pathogens/Roary/issues/132#issuecomment-111876254 .

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dutchscientist commented 9 years ago

There was no attachment by the way, but no worries. My testset is just a few ones I threw together.

andrewjpage commented 9 years ago

Hi Arnoud, 3.0.3 is in cpan now, sorry for the delay, I forgot to click a button. The attachment I sent didnt seem to come through on github. Andrew

On 15 June 2015 at 21:39, dutchscientist notifications@github.com wrote:

Hi Andrew,

CPAN still has 3.0.2 on it, while the website has 3.0.3? The "sudo cpanm -f Bio::Roary" command gives 3.0.2 (I have done sudo apt-get update).

Beers are always a good idea!

From: andrewjpage [mailto:notifications@github.com] Sent: 15 June 2015 14:42 To: sanger-pathogens/Roary Cc: dutchscientist Subject: Re: [Roary] Use of -e switch gives multifasta file with N's only (#132)

Hi Arnoud, I've tracked down the problem and fixed it. The latest version is 3.0.3. The parallel warning messages seem to be a bit of a red herring. Give it a whirl and let me know how you get along. I've attached the core gene alignment for your campy data. Thanks for all the helpful feedback and for your patience. If your ever over Cambridge direction, I'll buy you a pint or two. Andrew

On 14 June 2015 at 22:10, dutchscientist notifications@github.com wrote:

OK, very happy to do more tests, just remember, I am not a Linux expert. The instructions given were very helpful, that level I can do! ;-)

— Reply to this email directly or view it on GitHub < https://github.com/sanger-pathogens/Roary/issues/132#issuecomment-111876254

.

— Reply to this email directly or view it on GitHub < https://github.com/sanger-pathogens/Roary/issues/132#issuecomment-112074808> . < https://github.com/notifications/beacon/AJ8e0MaeDiDd9m9SsMvPOa6H--uSbPm4ks5oTs3BgaJpZM4Exndn.gif>

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dutchscientist commented 9 years ago 
                                                                                  No worries, will try today :-)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        From: andrewjpageSent: Tuesday, 16 June 2015 08:32To: sanger-pathogens/RoaryReply To: sanger-pathogens/RoaryCc: dutchscientistSubject: Re: [Roary] Use of -e switch gives multifasta file with N's only (#132)Hi Arnoud,

3.0.3 is in cpan now, sorry for the delay, I forgot to click a button. The attachment I sent didnt seem to come through on github. Andrew

On 15 June 2015 at 21:39, dutchscientist notifications@github.com wrote:

Hi Andrew,

CPAN still has 3.0.2 on it, while the website has 3.0.3? The "sudo cpanm -f Bio::Roary" command gives 3.0.2 (I have done sudo apt-get update).

Beers are always a good idea!

From: andrewjpage [mailto:notifications@github.com] Sent: 15 June 2015 14:42 To: sanger-pathogens/Roary Cc: dutchscientist Subject: Re: [Roary] Use of -e switch gives multifasta file with N's only (#132)

Hi Arnoud, I've tracked down the problem and fixed it. The latest version is 3.0.3. The parallel warning messages seem to be a bit of a red herring. Give it a whirl and let me know how you get along. I've attached the core gene alignment for your campy data. Thanks for all the helpful feedback and for your patience. If your ever over Cambridge direction, I'll buy you a pint or two. Andrew

On 14 June 2015 at 22:10, dutchscientist notifications@github.com wrote:

OK, very happy to do more tests, just remember, I am not a Linux expert. The instructions given were very helpful, that level I can do! ;-)

— Reply to this email directly or view it on GitHub < https://github.com/sanger-pathogens/Roary/issues/132#issuecomment-111876254

.

— Reply to this email directly or view it on GitHub < https://github.com/sanger-pathogens/Roary/issues/132#issuecomment-112074808> . < https://github.com/notifications/beacon/AJ8e0MaeDiDd9m9SsMvPOa6H--uSbPm4ks5oTs3BgaJpZM4Exndn.gif>

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dutchscientist commented 9 years ago

OK, installs fine but still the error message (from verbose output):

Failed test 'Actual output file exists gene_presence_absence.csv -j Parallel --dont_split_groups t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff '

at t/lib/TestHelper.pm line 176.

Wil give it a shot.

dutchscientist commented 9 years ago

It takes a while to produce the files, but works now, I get the core alignment :+1:

andrewjpage commented 9 years ago

Great thanks for letting me know. Yea the final step with aligning all the sequences takes quite a while, even longer now with prank, but luckily its paralleliseable. And thanks for all the feedback. Andrew

On 16 June 2015 at 13:43, dutchscientist notifications@github.com wrote:

It takes a while to produce the files, but works now, I get the core alignment [image: :+1:]

— Reply to this email directly or view it on GitHub https://github.com/sanger-pathogens/Roary/issues/132#issuecomment-112411517 .